chr4-110744627-T-C

Variant names:

• chr4-110744627-T-C
• rs2634073

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 0.693 in 151,716 control chromosomes in the GnomAD database, including 37,961 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 0.69 (37961 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.15
• Publications: 28 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.798 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.693 AC: 105127 AN: 151598 Hom.: 37944 Cov.: 30

Gnomad AFR AF: 0.583

Gnomad AMI AF: 0.928

Gnomad AMR AF: 0.593

Gnomad ASJ AF: 0.615

Gnomad EAS AF: 0.260

Gnomad SAS AF: 0.629

Gnomad FIN AF: 0.809

Gnomad MID AF: 0.696

Gnomad NFE AF: 0.803

Gnomad OTH AF: 0.700

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

GnomAD4 genome AF: 0.693 AC: 105173 AN: 151716 Hom.: 37961 Cov.: 30 AF XY: 0.682 AC XY: 50589 AN XY: 74134

African (AFR) AF: 0.582 AC: 24098 AN: 41392

American (AMR) AF: 0.593 AC: 8999 AN: 15186

Ashkenazi Jewish (ASJ) AF: 0.615 AC: 2129 AN: 3460

East Asian (EAS) AF: 0.259 AC: 1325 AN: 5114

South Asian (SAS) AF: 0.630 AC: 3028 AN: 4808

European-Finnish (FIN) AF: 0.809 AC: 8554 AN: 10572

Middle Eastern (MID) AF: 0.687 AC: 202 AN: 294

European-Non Finnish (NFE) AF: 0.803 AC: 54520 AN: 67872

Other (OTH) AF: 0.699 AC: 1472 AN: 2106

Alfa AF: 0.778 Hom.: 130242

Bravo AF: 0.672

Asia WGS AF: 0.469 AC: 1633 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	6.3
DANN	Benign	0.86
PhyloP100		1.1

Splicing

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

Other links and lift over

dbSNP: rs2634073; hg19: chr4-111665783;