chr4-31767096-T-A

Variant names:

• chr4-31767096-T-A
• rs10489006

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.132 in 152,200 control chromosomes in the GnomAD database, including 1,504 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 0.13 (1504 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.724

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.167 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

Frequencies

GnomAD3 genomes AF: 0.132 AC: 20110 AN: 152082 Hom.: 1502 Cov.: 32

Gnomad AFR AF: 0.171

Gnomad AMI AF: 0.112

Gnomad AMR AF: 0.0777

Gnomad ASJ AF: 0.140

Gnomad EAS AF: 0.00193

Gnomad SAS AF: 0.111

Gnomad FIN AF: 0.167

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.128

Gnomad OTH AF: 0.111

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

GnomAD4 genome AF: 0.132 AC: 20119 AN: 152200 Hom.: 1504 Cov.: 32 AF XY: 0.131 AC XY: 9722 AN XY: 74414

Gnomad4 AFR AF: 0.171

Gnomad4 AMR AF: 0.0776

Gnomad4 ASJ AF: 0.140

Gnomad4 EAS AF: 0.00193

Gnomad4 SAS AF: 0.111

Gnomad4 FIN AF: 0.167

Gnomad4 NFE AF: 0.128

Gnomad4 OTH AF: 0.110

Alfa AF: 0.133 Hom.: 176

Bravo AF: 0.128

Asia WGS AF: 0.0490 AC: 169 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.76
DANN	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10489006; hg19: chr4-31768718;