6-31605179-A-C

Variant names:

• chr6-31605179-A-C
• rs2844479

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 0.341 in 151,628 control chromosomes in the GnomAD database, including 9,238 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 0.34 (9238 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.468
• Publications: 102 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.442 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.342 AC: 51752 AN: 151510 Hom.: 9241 Cov.: 30

Gnomad AFR AF: 0.286

Gnomad AMI AF: 0.365

Gnomad AMR AF: 0.403

Gnomad ASJ AF: 0.590

Gnomad EAS AF: 0.458

Gnomad SAS AF: 0.334

Gnomad FIN AF: 0.288

Gnomad MID AF: 0.516

Gnomad NFE AF: 0.346

Gnomad OTH AF: 0.393

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

GnomAD4 genome AF: 0.341 AC: 51767 AN: 151628 Hom.: 9238 Cov.: 30 AF XY: 0.341 AC XY: 25286 AN XY: 74074

African (AFR) AF: 0.286 AC: 11809 AN: 41300

American (AMR) AF: 0.403 AC: 6125 AN: 15216

Ashkenazi Jewish (ASJ) AF: 0.590 AC: 2047 AN: 3468

East Asian (EAS) AF: 0.458 AC: 2346 AN: 5126

South Asian (SAS) AF: 0.334 AC: 1607 AN: 4808

European-Finnish (FIN) AF: 0.288 AC: 3032 AN: 10510

Middle Eastern (MID) AF: 0.517 AC: 151 AN: 292

European-Non Finnish (NFE) AF: 0.346 AC: 23494 AN: 67894

Other (OTH) AF: 0.392 AC: 825 AN: 2106

Alfa AF: 0.359 Hom.: 35182

Bravo AF: 0.349

Asia WGS AF: 0.376 AC: 1311 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	5.1
DANN	Benign	0.66
PhyloP100		0.47

Splicing

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

Other links and lift over

dbSNP: rs2844479; hg19: chr6-31572956;