10-133461854-T-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001396050.1(SCART1):​c.1969+1684T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.836 in 152,166 control chromosomes in the GnomAD database, including 53,516 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 0.84 ( 53516 hom., cov: 34)

Consequence

SCART1
NM_001396050.1 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.918
Variant links:
Genes affected
SCART1 (HGNC:32411): (scavenger receptor family member expressed on T cells 1) Predicted to enable scavenger receptor activity. Predicted to be involved in endocytosis. Located in brush border and cytoplasm. [provided by Alliance of Genome Resources, Apr 2022]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-1.0).
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.881 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
SCART1NM_001396050.1 linkc.1969+1684T>G intron_variant Intron 6 of 11 ENST00000640237.2 NP_001382979.1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
SCART1ENST00000640237.2 linkc.1969+1684T>G intron_variant Intron 6 of 11 5 NM_001396050.1 ENSP00000491516.1 Q4G0T1-1
SCART1ENST00000463137.5 linkn.2732+1684T>G intron_variant Intron 6 of 10 2
SCART1ENST00000482993.6 linkn.3114+1684T>G intron_variant Intron 5 of 9 2
SCART1ENST00000488261.6 linkn.2880+1684T>G intron_variant Intron 4 of 13 2

Frequencies

GnomAD3 genomes
AF:
0.836
AC:
127136
AN:
152048
Hom.:
53480
Cov.:
34
show subpopulations
Gnomad AFR
AF:
0.756
Gnomad AMI
AF:
0.751
Gnomad AMR
AF:
0.799
Gnomad ASJ
AF:
0.899
Gnomad EAS
AF:
0.743
Gnomad SAS
AF:
0.903
Gnomad FIN
AF:
0.894
Gnomad MID
AF:
0.946
Gnomad NFE
AF:
0.883
Gnomad OTH
AF:
0.857
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.836
AC:
127225
AN:
152166
Hom.:
53516
Cov.:
34
AF XY:
0.836
AC XY:
62220
AN XY:
74382
show subpopulations
Gnomad4 AFR
AF:
0.756
Gnomad4 AMR
AF:
0.799
Gnomad4 ASJ
AF:
0.899
Gnomad4 EAS
AF:
0.742
Gnomad4 SAS
AF:
0.903
Gnomad4 FIN
AF:
0.894
Gnomad4 NFE
AF:
0.883
Gnomad4 OTH
AF:
0.859
Alfa
AF:
0.877
Hom.:
22333
Bravo
AF:
0.825
Asia WGS
AF:
0.830
AC:
2888
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-1.0
CADD
Benign
2.5
DANN
Benign
0.24

Splicing

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: rs2252728; hg19: chr10-135275358; API