4-110748064-T-C

Variant names:

• chr4-110748064-T-C
• rs2634071

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 0.694 in 151,566 control chromosomes in the GnomAD database, including 37,944 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 (37944 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.434
• Publications: 15 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• 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: 0.694 AC: 105074 AN: 151448 Hom.: 37927 Cov.: 31

Gnomad AFR AF: 0.583

Gnomad AMI AF: 0.928

Gnomad AMR AF: 0.594

Gnomad ASJ AF: 0.616

Gnomad EAS AF: 0.263

Gnomad SAS AF: 0.630

Gnomad FIN AF: 0.809

Gnomad MID AF: 0.696

Gnomad NFE AF: 0.803

Gnomad OTH AF: 0.702

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

GnomAD4 genome AF: 0.694 AC: 105120 AN: 151566 Hom.: 37944 Cov.: 31 AF XY: 0.683 AC XY: 50573 AN XY: 74098

African (AFR) AF: 0.583 AC: 24099 AN: 41354

American (AMR) AF: 0.594 AC: 9012 AN: 15174

Ashkenazi Jewish (ASJ) AF: 0.616 AC: 2126 AN: 3454

East Asian (EAS) AF: 0.262 AC: 1347 AN: 5140

South Asian (SAS) AF: 0.631 AC: 3028 AN: 4802

European-Finnish (FIN) AF: 0.809 AC: 8566 AN: 10586

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

European-Non Finnish (NFE) AF: 0.803 AC: 54422 AN: 67750

Other (OTH) AF: 0.701 AC: 1472 AN: 2100

Alfa AF: 0.670 Hom.: 10925

Bravo AF: 0.673

Asia WGS AF: 0.468 AC: 1630 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.65
DANN	Benign	0.48
PhyloP100		-0.43

Splicing

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

Other links and lift over

dbSNP: rs2634071; hg19: chr4-111669220;