rs6831932

Variant names:

• chr4-25504310-T-C
• rs6831932

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 0.501 in 150,812 control chromosomes in the GnomAD database, including 19,934 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 0.50 (19934 hom., cov: 28)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0410
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.593 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: 0.501 AC: 75557 AN: 150722 Hom.: 19929 Cov.: 28

Gnomad AFR AF: 0.335

Gnomad AMI AF: 0.479

Gnomad AMR AF: 0.490

Gnomad ASJ AF: 0.591

Gnomad EAS AF: 0.411

Gnomad SAS AF: 0.530

Gnomad FIN AF: 0.547

Gnomad MID AF: 0.528

Gnomad NFE AF: 0.598

Gnomad OTH AF: 0.500

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

GnomAD4 genome AF: 0.501 AC: 75573 AN: 150812 Hom.: 19934 Cov.: 28 AF XY: 0.497 AC XY: 36533 AN XY: 73506

African (AFR) AF: 0.334 AC: 13702 AN: 40968

American (AMR) AF: 0.489 AC: 7410 AN: 15140

Ashkenazi Jewish (ASJ) AF: 0.591 AC: 2046 AN: 3464

East Asian (EAS) AF: 0.412 AC: 2099 AN: 5096

South Asian (SAS) AF: 0.532 AC: 2542 AN: 4782

European-Finnish (FIN) AF: 0.547 AC: 5575 AN: 10196

Middle Eastern (MID) AF: 0.541 AC: 159 AN: 294

European-Non Finnish (NFE) AF: 0.598 AC: 40562 AN: 67868

Other (OTH) AF: 0.498 AC: 1042 AN: 2094

Alfa AF: 0.573 Hom.: 42027

Bravo AF: 0.489

Asia WGS AF: 0.441 AC: 1535 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	6.0
DANN	Benign	0.64
PhyloP100		0.041

Splicing

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

Other links and lift over

dbSNP: rs6831932; hg19: chr4-25505932;