8-27921823-C-A

Variant summary

Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PP3

The NM_173833.6(SCARA5):​c.664G>T​(p.Asp222Tyr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000103 in 1,547,332 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: 𝑓 0.000092 ( 0 hom., cov: 34)
Exomes 𝑓: 0.0000014 ( 0 hom. )

Consequence

SCARA5
NM_173833.6 missense

Scores

6
9
4

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 1.47
Variant links:
Genes affected
SCARA5 (HGNC:28701): (scavenger receptor class A member 5) Predicted to enable ferritin receptor activity. Predicted to be involved in several processes, including cellular iron ion homeostasis; iron ion transmembrane transport; and protein homotrimerization. Predicted to act upstream of or within cellular response to heat. Predicted to be located in cell surface. Predicted to be integral component of plasma membrane. Predicted to be active in external side of plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 3 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
PP3
MetaRNN computational evidence supports a deleterious effect, 0.779

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
SCARA5NM_173833.6 linkc.664G>T p.Asp222Tyr missense_variant Exon 4 of 9 ENST00000354914.8 NP_776194.2 Q6ZMJ2-1
SCARA5NM_001413201.1 linkc.535G>T p.Asp179Tyr missense_variant Exon 3 of 8 NP_001400130.1
SCARA5NM_001413202.1 linkc.664G>T p.Asp222Tyr missense_variant Exon 4 of 7 NP_001400131.1
SCARA5NM_001413203.1 linkc.-141G>T 5_prime_UTR_variant Exon 3 of 8 NP_001400132.1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
SCARA5ENST00000354914.8 linkc.664G>T p.Asp222Tyr missense_variant Exon 4 of 9 2 NM_173833.6 ENSP00000346990.3 Q6ZMJ2-1
SCARA5ENST00000524352.5 linkc.664G>T p.Asp222Tyr missense_variant Exon 4 of 7 1 ENSP00000428663.1 Q6ZMJ2-2
SCARA5ENST00000518030.1 linkc.535G>T p.Asp179Tyr missense_variant Exon 2 of 5 1 ENSP00000430713.1 Q6ZMJ2-3
SCARA5ENST00000380385.6 linkc.242-12080G>T intron_variant Intron 3 of 7 1 ENSP00000369746.2 Q6ZMJ2-4

Frequencies

GnomAD3 genomes
AF:
0.0000920
AC:
14
AN:
152200
Hom.:
0
Cov.:
34
show subpopulations
Gnomad AFR
AF:
0.000338
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.00
Gnomad OTH
AF:
0.00
GnomAD3 exomes
AF:
0.00000686
AC:
1
AN:
145816
Hom.:
0
AF XY:
0.00
AC XY:
0
AN XY:
80048
show subpopulations
Gnomad AFR exome
AF:
0.000137
Gnomad AMR exome
AF:
0.00
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.00
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.00
Gnomad OTH exome
AF:
0.00
GnomAD4 exome
AF:
0.00000143
AC:
2
AN:
1395132
Hom.:
0
Cov.:
31
AF XY:
0.00
AC XY:
0
AN XY:
689560
show subpopulations
Gnomad4 AFR exome
AF:
0.0000638
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
AF:
0.0000920
AC:
14
AN:
152200
Hom.:
0
Cov.:
34
AF XY:
0.000108
AC XY:
8
AN XY:
74360
show subpopulations
Gnomad4 AFR
AF:
0.000338
Gnomad4 AMR
AF:
0.00
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.00
Gnomad4 OTH
AF:
0.00
Bravo
AF:
0.000159
ESP6500AA
AF:
0.000472
AC:
2
ESP6500EA
AF:
0.00
AC:
0
ExAC
AF:
0.00000881
AC:
1

ClinVar

Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not specified Uncertain:1
Dec 03, 2024
Ambry Genetics
Significance: Uncertain significance
Review Status: criteria provided, single submitter
Collection Method: clinical testing

The c.664G>T (p.D222Y) alteration is located in exon 4 (coding exon 3) of the SCARA5 gene. This alteration results from a G to T substitution at nucleotide position 664, causing the aspartic acid (D) at amino acid position 222 to be replaced by a tyrosine (Y). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Uncertain
0.45
BayesDel_addAF
Pathogenic
0.19
D
BayesDel_noAF
Uncertain
0.040
CADD
Uncertain
24
DANN
Uncertain
0.99
DEOGEN2
Benign
0.25
T;.;.
Eigen
Uncertain
0.48
Eigen_PC
Uncertain
0.42
FATHMM_MKL
Uncertain
0.78
D
LIST_S2
Benign
0.81
T;T;T
M_CAP
Pathogenic
0.50
D
MetaRNN
Pathogenic
0.78
D;D;D
MetaSVM
Pathogenic
0.97
D
MutationAssessor
Benign
1.6
L;L;.
PrimateAI
Pathogenic
0.80
T
PROVEAN
Uncertain
-3.7
D;D;D
REVEL
Pathogenic
0.69
Sift
Uncertain
0.0020
D;D;D
Sift4G
Uncertain
0.0030
D;D;D
Polyphen
0.99
D;D;D
Vest4
0.57
MVP
0.98
MPC
0.92
ClinPred
0.78
D
GERP RS
4.9
Varity_R
0.43
gMVP
0.58

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs373937854; hg19: chr8-27779340; API