rs2634073

chr4-110744627-T-C

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 0.693 in 151,716 control chromosomes in the GnomAD database, including 37,961 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 (37961 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.15

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• 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/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.693 AC: 105127 AN: 151598 Hom.: 37944 Cov.: 30

Gnomad AFR AF: 0.583

Gnomad AMI AF: 0.928

Gnomad AMR AF: 0.593

Gnomad ASJ AF: 0.615

Gnomad EAS AF: 0.260

Gnomad SAS AF: 0.629

Gnomad FIN AF: 0.809

Gnomad MID AF: 0.696

Gnomad NFE AF: 0.803

Gnomad OTH AF: 0.700

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

GnomAD4 genome AF: 0.693 AC: 105173 AN: 151716 Hom.: 37961 Cov.: 30 AF XY: 0.682 AC XY: 50589 AN XY: 74134

Gnomad4 AFR AF: 0.582

Gnomad4 AMR AF: 0.593

Gnomad4 ASJ AF: 0.615

Gnomad4 EAS AF: 0.259

Gnomad4 SAS AF: 0.630

Gnomad4 FIN AF: 0.809

Gnomad4 NFE AF: 0.803

Gnomad4 OTH AF: 0.699

Alfa AF: 0.782 Hom.: 58447

Bravo AF: 0.672

Asia WGS AF: 0.469 AC: 1633 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
Cadd	Benign	6.3
Dann	Benign	0.86

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2634073; hg19: chr4-111665783;