6-31107704-A-G

Variant names:

• chr6-31107704-A-G
• rs2844635

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 0.368 in 152,022 control chromosomes in the GnomAD database, including 10,723 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 0.37 (10723 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.298
• Publications: 27 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.437 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.368 AC: 55933 AN: 151904 Hom.: 10710 Cov.: 32

Gnomad AFR AF: 0.442

Gnomad AMI AF: 0.367

Gnomad AMR AF: 0.358

Gnomad ASJ AF: 0.556

Gnomad EAS AF: 0.0997

Gnomad SAS AF: 0.313

Gnomad FIN AF: 0.368

Gnomad MID AF: 0.430

Gnomad NFE AF: 0.339

Gnomad OTH AF: 0.407

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

GnomAD4 genome AF: 0.368 AC: 55976 AN: 152022 Hom.: 10723 Cov.: 32 AF XY: 0.365 AC XY: 27133 AN XY: 74310

African (AFR) AF: 0.442 AC: 18323 AN: 41420

American (AMR) AF: 0.358 AC: 5470 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.556 AC: 1929 AN: 3468

East Asian (EAS) AF: 0.0999 AC: 518 AN: 5186

South Asian (SAS) AF: 0.314 AC: 1511 AN: 4816

European-Finnish (FIN) AF: 0.368 AC: 3890 AN: 10566

Middle Eastern (MID) AF: 0.425 AC: 125 AN: 294

European-Non Finnish (NFE) AF: 0.339 AC: 23027 AN: 67972

Other (OTH) AF: 0.403 AC: 850 AN: 2108

Alfa AF: 0.354 Hom.: 28363

Bravo AF: 0.372

Asia WGS AF: 0.247 AC: 863 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.3
DANN	Benign	0.62
PhyloP100		-0.30

Splicing

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

Other links and lift over

dbSNP: rs2844635; hg19: chr6-31075481;