rs6831932

Variant names:

• chr4-25504310-T-C
• rs6831932

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 0.501 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.501 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

Gnomad4 AFR AF: 0.334

Gnomad4 AMR AF: 0.489

Gnomad4 ASJ AF: 0.591

Gnomad4 EAS AF: 0.412

Gnomad4 SAS AF: 0.532

Gnomad4 FIN AF: 0.547

Gnomad4 NFE AF: 0.598

Gnomad4 OTH AF: 0.498

Alfa AF: 0.579 Hom.: 30127

Bravo AF: 0.489

Asia WGS AF: 0.441 AC: 1535 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6831932; hg19: chr4-25505932;