chr4-31935842-G-A

Variant names:

• chr4-31935842-G-A
• rs17799612

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 0.0665 in 151,754 control chromosomes in the GnomAD database, including 369 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 0.066 (369 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.378
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0849 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: 0.0664 AC: 10076 AN: 151636 Hom.: 368 Cov.: 32

Gnomad AFR AF: 0.0523

Gnomad AMI AF: 0.114

Gnomad AMR AF: 0.0578

Gnomad ASJ AF: 0.0379

Gnomad EAS AF: 0.00847

Gnomad SAS AF: 0.0522

Gnomad FIN AF: 0.0457

Gnomad MID AF: 0.0255

Gnomad NFE AF: 0.0868

Gnomad OTH AF: 0.0629

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

GnomAD4 genome AF: 0.0665 AC: 10086 AN: 151754 Hom.: 369 Cov.: 32 AF XY: 0.0633 AC XY: 4694 AN XY: 74160

African (AFR) AF: 0.0523 AC: 2164 AN: 41378

American (AMR) AF: 0.0578 AC: 878 AN: 15198

Ashkenazi Jewish (ASJ) AF: 0.0379 AC: 131 AN: 3460

East Asian (EAS) AF: 0.00849 AC: 44 AN: 5180

South Asian (SAS) AF: 0.0525 AC: 253 AN: 4822

European-Finnish (FIN) AF: 0.0457 AC: 481 AN: 10514

Middle Eastern (MID) AF: 0.0205 AC: 6 AN: 292

European-Non Finnish (NFE) AF: 0.0868 AC: 5890 AN: 67894

Other (OTH) AF: 0.0642 AC: 135 AN: 2104

Alfa AF: 0.0802 Hom.: 353

Bravo AF: 0.0652

Asia WGS AF: 0.0310 AC: 111 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.4
DANN	Benign	0.71
PhyloP100		-0.38

Splicing

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

Other links and lift over

dbSNP: rs17799612; hg19: chr4-31937464;