4-110844339-C-T

Variant names:

• chr4-110844339-C-T
• rs6838973

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 0.378 in 151,910 control chromosomes in the GnomAD database, including 11,972 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 0.38 (11972 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.303
• Publications: 22 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.564 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: 0.378 AC: 57450 AN: 151794 Hom.: 11975 Cov.: 31

Gnomad AFR AF: 0.207

Gnomad AMI AF: 0.314

Gnomad AMR AF: 0.416

Gnomad ASJ AF: 0.377

Gnomad EAS AF: 0.583

Gnomad SAS AF: 0.572

Gnomad FIN AF: 0.501

Gnomad MID AF: 0.358

Gnomad NFE AF: 0.427

Gnomad OTH AF: 0.375

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

GnomAD4 genome AF: 0.378 AC: 57451 AN: 151910 Hom.: 11972 Cov.: 31 AF XY: 0.384 AC XY: 28521 AN XY: 74232

African (AFR) AF: 0.206 AC: 8560 AN: 41472

American (AMR) AF: 0.416 AC: 6349 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.377 AC: 1307 AN: 3468

East Asian (EAS) AF: 0.582 AC: 2994 AN: 5146

South Asian (SAS) AF: 0.573 AC: 2757 AN: 4814

European-Finnish (FIN) AF: 0.501 AC: 5278 AN: 10526

Middle Eastern (MID) AF: 0.371 AC: 109 AN: 294

European-Non Finnish (NFE) AF: 0.427 AC: 29019 AN: 67934

Other (OTH) AF: 0.377 AC: 792 AN: 2100

Alfa AF: 0.420 Hom.: 58382

Bravo AF: 0.364

Asia WGS AF: 0.528 AC: 1837 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.8
DANN	Benign	0.50
PhyloP100		-0.30

Splicing

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

Other links and lift over

dbSNP: rs6838973; hg19: chr4-111765495;