4-74112120-T-C

Variant names:

• chr4-74112120-T-C
• rs1371799

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 0.497 in 151,996 control chromosomes in the GnomAD database, including 21,280 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 0.50 (21280 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.306
• Publications: 17 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 (AMR) allele frequency at 95% confidence interval = 0.616 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: 0.498 AC: 75591 AN: 151876 Hom.: 21280 Cov.: 31

Gnomad AFR AF: 0.221

Gnomad AMI AF: 0.668

Gnomad AMR AF: 0.626

Gnomad ASJ AF: 0.583

Gnomad EAS AF: 0.336

Gnomad SAS AF: 0.547

Gnomad FIN AF: 0.664

Gnomad MID AF: 0.525

Gnomad NFE AF: 0.612

Gnomad OTH AF: 0.524

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

GnomAD4 genome AF: 0.497 AC: 75599 AN: 151996 Hom.: 21280 Cov.: 31 AF XY: 0.502 AC XY: 37322 AN XY: 74294

African (AFR) AF: 0.221 AC: 9147 AN: 41462

American (AMR) AF: 0.626 AC: 9561 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.583 AC: 2022 AN: 3468

East Asian (EAS) AF: 0.337 AC: 1732 AN: 5140

South Asian (SAS) AF: 0.547 AC: 2631 AN: 4808

European-Finnish (FIN) AF: 0.664 AC: 7021 AN: 10570

Middle Eastern (MID) AF: 0.527 AC: 154 AN: 292

European-Non Finnish (NFE) AF: 0.612 AC: 41622 AN: 67960

Other (OTH) AF: 0.520 AC: 1100 AN: 2114

Alfa AF: 0.573 Hom.: 17700

Bravo AF: 0.483

Asia WGS AF: 0.404 AC: 1407 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	5.5
DANN	Benign	0.73
PhyloP100		0.31

Splicing

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

Other links and lift over

dbSNP: rs1371799; hg19: chr4-74977837;