4-103735913-T-G

Variant names:

• chr4-103735913-T-G
• rs233992

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 0.601 in 151,870 control chromosomes in the GnomAD database, including 29,998 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 0.60 (29998 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0230
• Publications: 3 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 (AFR) allele frequency at 95% confidence interval = 0.862 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: 0.601 AC: 91176 AN: 151748 Hom.: 29950 Cov.: 30

Gnomad AFR AF: 0.870

Gnomad AMI AF: 0.404

Gnomad AMR AF: 0.623

Gnomad ASJ AF: 0.526

Gnomad EAS AF: 0.731

Gnomad SAS AF: 0.570

Gnomad FIN AF: 0.534

Gnomad MID AF: 0.449

Gnomad NFE AF: 0.444

Gnomad OTH AF: 0.559

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

GnomAD4 genome AF: 0.601 AC: 91285 AN: 151870 Hom.: 29998 Cov.: 30 AF XY: 0.605 AC XY: 44922 AN XY: 74210

African (AFR) AF: 0.870 AC: 36033 AN: 41428

American (AMR) AF: 0.623 AC: 9483 AN: 15228

Ashkenazi Jewish (ASJ) AF: 0.526 AC: 1826 AN: 3472

East Asian (EAS) AF: 0.729 AC: 3746 AN: 5136

South Asian (SAS) AF: 0.569 AC: 2740 AN: 4814

European-Finnish (FIN) AF: 0.534 AC: 5633 AN: 10558

Middle Eastern (MID) AF: 0.435 AC: 128 AN: 294

European-Non Finnish (NFE) AF: 0.444 AC: 30145 AN: 67916

Other (OTH) AF: 0.560 AC: 1183 AN: 2112

Alfa AF: 0.493 Hom.: 81875

Bravo AF: 0.622

Asia WGS AF: 0.630 AC: 2189 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	1.2
DANN	Benign	0.59
PhyloP100		-0.023

Splicing

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

Other links and lift over

dbSNP: rs233992; hg19: chr4-104657070;