10-31588492-T-C

Variant names:

• chr10-31588492-T-C
• rs4747753
• ENST00000829893.1:n.310+15271A>G

Variant summary

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

The ENST00000829893.1(ENSG00000307931):​n.310+15271A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.482 in 151,940 control chromosomes in the GnomAD database, including 21,079 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 0.48 (21079 hom., cov: 31)
• Consequence: ENSG00000307931 ENST00000829893.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.493
• Publications: 1 publications found

Genes affected

ENSG00000307931 (HGNC:):

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 (NFE) allele frequency at 95% confidence interval = 0.651 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000307931	ENST00000829893.1	n.310+15271A>G		intron_variant	Intron 1 of 1
ENSG00000223834	ENST00000830032.1	n.246+1232T>C		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.482 AC: 73240 AN: 151822 Hom.: 21063 Cov.: 31

Gnomad AFR AF: 0.160

Gnomad AMI AF: 0.558

Gnomad AMR AF: 0.593

Gnomad ASJ AF: 0.536

Gnomad EAS AF: 0.371

Gnomad SAS AF: 0.436

Gnomad FIN AF: 0.514

Gnomad MID AF: 0.547

Gnomad NFE AF: 0.656

Gnomad OTH AF: 0.491

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

GnomAD4 genome AF: 0.482 AC: 73264 AN: 151940 Hom.: 21079 Cov.: 31 AF XY: 0.476 AC XY: 35358 AN XY: 74260

African (AFR) AF: 0.160 AC: 6634 AN: 41464

American (AMR) AF: 0.593 AC: 9061 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.536 AC: 1861 AN: 3470

East Asian (EAS) AF: 0.372 AC: 1914 AN: 5152

South Asian (SAS) AF: 0.436 AC: 2104 AN: 4822

European-Finnish (FIN) AF: 0.514 AC: 5421 AN: 10548

Middle Eastern (MID) AF: 0.565 AC: 166 AN: 294

European-Non Finnish (NFE) AF: 0.656 AC: 44557 AN: 67894

Other (OTH) AF: 0.492 AC: 1039 AN: 2112

Alfa AF: 0.538 Hom.: 3197

Bravo AF: 0.478

Asia WGS AF: 0.371 AC: 1293 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	1.7
DANN	Benign	0.80
PhyloP100		-0.49

Splicing

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

Other links and lift over

dbSNP: rs4747753; hg19: chr10-31877420; COSMIC: COSV66495039;