2-4657673-T-C

Position:

• chr2-4657673-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 0.854 in 152,170 control chromosomes in the GnomAD database, including 55,966 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 0.85 (55966 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.08

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.951 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: 0.854 AC: 129882 AN: 152052 Hom.: 55902 Cov.: 32

Gnomad AFR AF: 0.958

Gnomad AMI AF: 0.640

Gnomad AMR AF: 0.891

Gnomad ASJ AF: 0.705

Gnomad EAS AF: 0.749

Gnomad SAS AF: 0.764

Gnomad FIN AF: 0.801

Gnomad MID AF: 0.804

Gnomad NFE AF: 0.816

Gnomad OTH AF: 0.844

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

GnomAD4 genome AF: 0.854 AC: 130008 AN: 152170 Hom.: 55966 Cov.: 32 AF XY: 0.852 AC XY: 63364 AN XY: 74390

Gnomad4 AFR AF: 0.958

Gnomad4 AMR AF: 0.891

Gnomad4 ASJ AF: 0.705

Gnomad4 EAS AF: 0.749

Gnomad4 SAS AF: 0.765

Gnomad4 FIN AF: 0.801

Gnomad4 NFE AF: 0.816

Gnomad4 OTH AF: 0.843

Alfa AF: 0.817 Hom.: 78060

Bravo AF: 0.866

Asia WGS AF: 0.745 AC: 2589 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.34
DANN	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs699549; hg19: chr2-4705263;