chr4-24734635-T-G

Variant names:

• chr4-24734635-T-G
• rs1476880

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 0.606 in 152,128 control chromosomes in the GnomAD database, including 28,265 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 0.61 (28265 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.19
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.702 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: 0.606 AC: 92118 AN: 152010 Hom.: 28229 Cov.: 33

Gnomad AFR AF: 0.708

Gnomad AMI AF: 0.668

Gnomad AMR AF: 0.602

Gnomad ASJ AF: 0.614

Gnomad EAS AF: 0.602

Gnomad SAS AF: 0.678

Gnomad FIN AF: 0.533

Gnomad MID AF: 0.551

Gnomad NFE AF: 0.550

Gnomad OTH AF: 0.610

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

GnomAD4 genome AF: 0.606 AC: 92209 AN: 152128 Hom.: 28265 Cov.: 33 AF XY: 0.609 AC XY: 45253 AN XY: 74362

African (AFR) AF: 0.709 AC: 29400 AN: 41496

American (AMR) AF: 0.603 AC: 9215 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.614 AC: 2131 AN: 3472

East Asian (EAS) AF: 0.600 AC: 3104 AN: 5170

South Asian (SAS) AF: 0.677 AC: 3266 AN: 4826

European-Finnish (FIN) AF: 0.533 AC: 5629 AN: 10556

Middle Eastern (MID) AF: 0.548 AC: 161 AN: 294

European-Non Finnish (NFE) AF: 0.550 AC: 37417 AN: 67998

Other (OTH) AF: 0.605 AC: 1278 AN: 2112

Alfa AF: 0.568 Hom.: 108061

Bravo AF: 0.614

Asia WGS AF: 0.636 AC: 2211 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.20
DANN	Benign	0.48
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs1476880; hg19: chr4-24736258;