10-133461854-T-G
Variant names:
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
NM_001396050.1 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.918
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 |
---|---|---|---|---|---|---|---|---|
SCART1 | NM_001396050.1 | c.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 |
---|---|---|---|---|---|---|---|---|---|---|
SCART1 | ENST00000640237.2 | c.1969+1684T>G | intron_variant | Intron 6 of 11 | 5 | NM_001396050.1 | ENSP00000491516.1 | |||
SCART1 | ENST00000463137.5 | n.2732+1684T>G | intron_variant | Intron 6 of 10 | 2 | |||||
SCART1 | ENST00000482993.6 | n.3114+1684T>G | intron_variant | Intron 5 of 9 | 2 | |||||
SCART1 | ENST00000488261.6 | n.2880+1684T>G | intron_variant | Intron 4 of 13 | 2 |
Frequencies
GnomAD3 genomes AF: 0.836 AC: 127136AN: 152048Hom.: 53480 Cov.: 34
GnomAD3 genomes
AF:
AC:
127136
AN:
152048
Hom.:
Cov.:
34
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.836 AC: 127225AN: 152166Hom.: 53516 Cov.: 34 AF XY: 0.836 AC XY: 62220AN XY: 74382
GnomAD4 genome
AF:
AC:
127225
AN:
152166
Hom.:
Cov.:
34
AF XY:
AC XY:
62220
AN XY:
74382
Gnomad4 AFR
AF:
Gnomad4 AMR
AF:
Gnomad4 ASJ
AF:
Gnomad4 EAS
AF:
Gnomad4 SAS
AF:
Gnomad4 FIN
AF:
Gnomad4 NFE
AF:
Gnomad4 OTH
AF:
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
2888
AN:
3478
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at