chr8-27951477-T-G

Variant names:

• chr8-27951477-T-G
• rs10866867
• NM_173833.6:c.241+14937A>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_173833.6(SCARA5):​c.241+14937A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.705 in 152,118 control chromosomes in the GnomAD database, including 38,256 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.70 (38256 hom., cov: 33)
• Consequence: SCARA5 NM_173833.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.309
• Publications: 8 publications found

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]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.856 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SCARA5	NM_173833.6	c.241+14937A>C		intron_variant	Intron 3 of 8	ENST00000354914.8	NP_776194.2
SCARA5	NM_001413201.1	c.113-29232A>C		intron_variant	Intron 2 of 7		NP_001400130.1
SCARA5	NM_001413202.1	c.241+14937A>C		intron_variant	Intron 3 of 6		NP_001400131.1
SCARA5	NM_001413203.1	c.-564+14937A>C		intron_variant	Intron 2 of 7		NP_001400132.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SCARA5	ENST00000354914.8	c.241+14937A>C		intron_variant	Intron 3 of 8	2	NM_173833.6	ENSP00000346990.3
SCARA5	ENST00000524352.5	c.241+14937A>C		intron_variant	Intron 3 of 6	1		ENSP00000428663.1
SCARA5	ENST00000518030.1	c.113-29232A>C		intron_variant	Intron 1 of 4	1		ENSP00000430713.1
SCARA5	ENST00000380385.6	c.241+14937A>C		intron_variant	Intron 3 of 7	1		ENSP00000369746.2

Frequencies

GnomAD3 genomes AF: 0.705 AC: 107115 AN: 152000 Hom.: 38228 Cov.: 33

Gnomad AFR AF: 0.597

Gnomad AMI AF: 0.570

Gnomad AMR AF: 0.788

Gnomad ASJ AF: 0.842

Gnomad EAS AF: 0.807

Gnomad SAS AF: 0.879

Gnomad FIN AF: 0.696

Gnomad MID AF: 0.867

Gnomad NFE AF: 0.726

Gnomad OTH AF: 0.732

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.705 AC: 107199 AN: 152118 Hom.: 38256 Cov.: 33 AF XY: 0.710 AC XY: 52809 AN XY: 74380

African (AFR) AF: 0.598 AC: 24804 AN: 41494

American (AMR) AF: 0.788 AC: 12057 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.842 AC: 2921 AN: 3470

East Asian (EAS) AF: 0.808 AC: 4172 AN: 5166

South Asian (SAS) AF: 0.878 AC: 4234 AN: 4824

European-Finnish (FIN) AF: 0.696 AC: 7370 AN: 10584

Middle Eastern (MID) AF: 0.867 AC: 255 AN: 294

European-Non Finnish (NFE) AF: 0.726 AC: 49327 AN: 67976

Other (OTH) AF: 0.731 AC: 1539 AN: 2106

Alfa AF: 0.726 Hom.: 125846

Bravo AF: 0.703

Asia WGS AF: 0.827 AC: 2876 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.1
DANN	Benign	0.76
PhyloP100		-0.31
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs10866867; hg19: chr8-27808994;