4-6734337-T-C

Variant names:

• chr4-6734337-T-C
• rs4626203

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 0.437 in 151,996 control chromosomes in the GnomAD database, including 15,344 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 0.44 (15344 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.31
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.591 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: 0.437 AC: 66402 AN: 151878 Hom.: 15313 Cov.: 32

Gnomad AFR AF: 0.597

Gnomad AMI AF: 0.342

Gnomad AMR AF: 0.459

Gnomad ASJ AF: 0.420

Gnomad EAS AF: 0.387

Gnomad SAS AF: 0.353

Gnomad FIN AF: 0.378

Gnomad MID AF: 0.382

Gnomad NFE AF: 0.357

Gnomad OTH AF: 0.423

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

GnomAD4 genome AF: 0.437 AC: 66478 AN: 151996 Hom.: 15344 Cov.: 32 AF XY: 0.436 AC XY: 32379 AN XY: 74278

African (AFR) AF: 0.597 AC: 24767 AN: 41456

American (AMR) AF: 0.458 AC: 6998 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.420 AC: 1457 AN: 3470

East Asian (EAS) AF: 0.387 AC: 1996 AN: 5154

South Asian (SAS) AF: 0.352 AC: 1697 AN: 4816

European-Finnish (FIN) AF: 0.378 AC: 3995 AN: 10564

Middle Eastern (MID) AF: 0.394 AC: 115 AN: 292

European-Non Finnish (NFE) AF: 0.357 AC: 24255 AN: 67944

Other (OTH) AF: 0.420 AC: 886 AN: 2108

Alfa AF: 0.375 Hom.: 22411

Bravo AF: 0.452

Asia WGS AF: 0.372 AC: 1292 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.87
DANN	Benign	0.33
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs4626203; hg19: chr4-6736064;