rs10489006

Variant names:

• chr4-31767096-T-A
• rs10489006

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.171 AC: 7080 AN: 41522

American (AMR) AF: 0.0776 AC: 1186 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.140 AC: 487 AN: 3472

East Asian (EAS) AF: 0.00193 AC: 10 AN: 5182

South Asian (SAS) AF: 0.111 AC: 537 AN: 4828

European-Finnish (FIN) AF: 0.167 AC: 1762 AN: 10580

Middle Eastern (MID) AF: 0.102 AC: 30 AN: 294

European-Non Finnish (NFE) AF: 0.128 AC: 8693 AN: 68010

Other (OTH) AF: 0.110 AC: 232 AN: 2110

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.76
DANN	Benign	0.45
PhyloP100		-0.72

Splicing

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

Other links and lift over

dbSNP: rs10489006; hg19: chr4-31768718;