4-81356502-C-G

Variant names:

• chr4-81356502-C-G
• rs725826

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 0.41 in 151,914 control chromosomes in the GnomAD database, including 16,464 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 0.41 (16464 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.812
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.751 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: 0.410 AC: 62258 AN: 151796 Hom.: 16429 Cov.: 31

Gnomad AFR AF: 0.758

Gnomad AMI AF: 0.261

Gnomad AMR AF: 0.324

Gnomad ASJ AF: 0.269

Gnomad EAS AF: 0.180

Gnomad SAS AF: 0.216

Gnomad FIN AF: 0.253

Gnomad MID AF: 0.316

Gnomad NFE AF: 0.285

Gnomad OTH AF: 0.362

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

GnomAD4 genome AF: 0.410 AC: 62349 AN: 151914 Hom.: 16464 Cov.: 31 AF XY: 0.401 AC XY: 29796 AN XY: 74232

African (AFR) AF: 0.758 AC: 31400 AN: 41442

American (AMR) AF: 0.324 AC: 4943 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.269 AC: 933 AN: 3464

East Asian (EAS) AF: 0.181 AC: 934 AN: 5170

South Asian (SAS) AF: 0.217 AC: 1042 AN: 4808

European-Finnish (FIN) AF: 0.253 AC: 2668 AN: 10540

Middle Eastern (MID) AF: 0.310 AC: 91 AN: 294

European-Non Finnish (NFE) AF: 0.285 AC: 19346 AN: 67926

Other (OTH) AF: 0.358 AC: 754 AN: 2104

Alfa AF: 0.179 Hom.: 319

Bravo AF: 0.432

Asia WGS AF: 0.209 AC: 730 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.23
DANN	Benign	0.41
PhyloP100		-0.81

Splicing

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

Other links and lift over

dbSNP: rs725826; hg19: chr4-82277656;