4-34991039-G-A

Variant names:

• chr4-34991039-G-A
• rs16990620

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 0.184 in 152,008 control chromosomes in the GnomAD database, including 2,863 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 0.18 (2863 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.55
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.308 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: 0.184 AC: 27873 AN: 151890 Hom.: 2854 Cov.: 32

Gnomad AFR AF: 0.263

Gnomad AMI AF: 0.288

Gnomad AMR AF: 0.179

Gnomad ASJ AF: 0.194

Gnomad EAS AF: 0.320

Gnomad SAS AF: 0.165

Gnomad FIN AF: 0.119

Gnomad MID AF: 0.313

Gnomad NFE AF: 0.134

Gnomad OTH AF: 0.190

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

GnomAD4 genome AF: 0.184 AC: 27915 AN: 152008 Hom.: 2863 Cov.: 32 AF XY: 0.185 AC XY: 13738 AN XY: 74282

African (AFR) AF: 0.263 AC: 10917 AN: 41448

American (AMR) AF: 0.180 AC: 2746 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.194 AC: 671 AN: 3466

East Asian (EAS) AF: 0.320 AC: 1655 AN: 5166

South Asian (SAS) AF: 0.166 AC: 798 AN: 4818

European-Finnish (FIN) AF: 0.119 AC: 1251 AN: 10552

Middle Eastern (MID) AF: 0.303 AC: 89 AN: 294

European-Non Finnish (NFE) AF: 0.134 AC: 9122 AN: 67978

Other (OTH) AF: 0.191 AC: 403 AN: 2112

Alfa AF: 0.154 Hom.: 7647

Bravo AF: 0.195

Asia WGS AF: 0.231 AC: 807 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.20
DANN	Benign	0.22
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs16990620; hg19: chr4-34992661;