4-110798529-A-G

Variant names:

• chr4-110798529-A-G
• rs11931959

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 0.393 in 151,948 control chromosomes in the GnomAD database, including 12,769 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 0.39 (12769 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.496
• Publications: 9 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.65 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: 0.393 AC: 59596 AN: 151830 Hom.: 12748 Cov.: 32

Gnomad AFR AF: 0.518

Gnomad AMI AF: 0.287

Gnomad AMR AF: 0.443

Gnomad ASJ AF: 0.480

Gnomad EAS AF: 0.668

Gnomad SAS AF: 0.365

Gnomad FIN AF: 0.306

Gnomad MID AF: 0.437

Gnomad NFE AF: 0.296

Gnomad OTH AF: 0.392

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

GnomAD4 genome AF: 0.393 AC: 59661 AN: 151948 Hom.: 12769 Cov.: 32 AF XY: 0.397 AC XY: 29478 AN XY: 74262

African (AFR) AF: 0.518 AC: 21441 AN: 41412

American (AMR) AF: 0.444 AC: 6774 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.480 AC: 1665 AN: 3468

East Asian (EAS) AF: 0.669 AC: 3441 AN: 5146

South Asian (SAS) AF: 0.364 AC: 1748 AN: 4808

European-Finnish (FIN) AF: 0.306 AC: 3236 AN: 10572

Middle Eastern (MID) AF: 0.439 AC: 129 AN: 294

European-Non Finnish (NFE) AF: 0.296 AC: 20146 AN: 67964

Other (OTH) AF: 0.390 AC: 820 AN: 2104

Alfa AF: 0.331 Hom.: 34061

Bravo AF: 0.412

Asia WGS AF: 0.462 AC: 1607 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	5.2
DANN	Benign	0.57
PhyloP100		0.50

Splicing

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

Other links and lift over

dbSNP: rs11931959; hg19: chr4-111719685;