4-71695463-G-T

Variant names:

• chr4-71695463-G-T
• rs423817

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 0.318 in 152,014 control chromosomes in the GnomAD database, including 8,252 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 0.32 (8252 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0220
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.543 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: 0.318 AC: 48273 AN: 151896 Hom.: 8255 Cov.: 32

Gnomad AFR AF: 0.408

Gnomad AMI AF: 0.221

Gnomad AMR AF: 0.326

Gnomad ASJ AF: 0.248

Gnomad EAS AF: 0.560

Gnomad SAS AF: 0.431

Gnomad FIN AF: 0.261

Gnomad MID AF: 0.326

Gnomad NFE AF: 0.249

Gnomad OTH AF: 0.314

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

GnomAD4 genome AF: 0.318 AC: 48298 AN: 152014 Hom.: 8252 Cov.: 32 AF XY: 0.322 AC XY: 23918 AN XY: 74314

African (AFR) AF: 0.408 AC: 16894 AN: 41444

American (AMR) AF: 0.326 AC: 4986 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.248 AC: 861 AN: 3466

East Asian (EAS) AF: 0.560 AC: 2880 AN: 5144

South Asian (SAS) AF: 0.431 AC: 2071 AN: 4810

European-Finnish (FIN) AF: 0.261 AC: 2761 AN: 10572

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

European-Non Finnish (NFE) AF: 0.248 AC: 16891 AN: 67972

Other (OTH) AF: 0.312 AC: 661 AN: 2116

Alfa AF: 0.235 Hom.: 1618

Bravo AF: 0.328

Asia WGS AF: 0.466 AC: 1617 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	4.5
DANN	Benign	0.52
PhyloP100		-0.022

Splicing

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

Other links and lift over

dbSNP: rs423817; hg19: chr4-72561180;