4-103497082-G-T

Position:

• chr4-103497082-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.594 in 151,886 control chromosomes in the GnomAD database, including 30,470 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 0.59 (30470 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.187

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.9 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.594 AC: 90146 AN: 151768 Hom.: 30455 Cov.: 31

Gnomad AFR AF: 0.249

Gnomad AMI AF: 0.733

Gnomad AMR AF: 0.719

Gnomad ASJ AF: 0.698

Gnomad EAS AF: 0.923

Gnomad SAS AF: 0.720

Gnomad FIN AF: 0.712

Gnomad MID AF: 0.580

Gnomad NFE AF: 0.716

Gnomad OTH AF: 0.615

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

GnomAD4 genome AF: 0.594 AC: 90180 AN: 151886 Hom.: 30470 Cov.: 31 AF XY: 0.602 AC XY: 44657 AN XY: 74190

Gnomad4 AFR AF: 0.249

Gnomad4 AMR AF: 0.720

Gnomad4 ASJ AF: 0.698

Gnomad4 EAS AF: 0.922

Gnomad4 SAS AF: 0.720

Gnomad4 FIN AF: 0.712

Gnomad4 NFE AF: 0.716

Gnomad4 OTH AF: 0.619

Alfa AF: 0.693 Hom.: 47242

Bravo AF: 0.580

Asia WGS AF: 0.760 AC: 2644 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	2.5
DANN	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs340468; hg19: chr4-104418239;