chr2-57287706-C-A

Position:

• chr2-57287706-C-A

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 0.139 in 152,004 control chromosomes in the GnomAD database, including 1,913 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 0.14 (1913 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.620

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.352 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: 0.139 AC: 21060 AN: 151884 Hom.: 1910 Cov.: 32

Gnomad AFR AF: 0.227

Gnomad AMI AF: 0.0548

Gnomad AMR AF: 0.0759

Gnomad ASJ AF: 0.137

Gnomad EAS AF: 0.365

Gnomad SAS AF: 0.114

Gnomad FIN AF: 0.159

Gnomad MID AF: 0.115

Gnomad NFE AF: 0.0822

Gnomad OTH AF: 0.123

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

GnomAD4 genome AF: 0.139 AC: 21071 AN: 152004 Hom.: 1913 Cov.: 32 AF XY: 0.143 AC XY: 10624 AN XY: 74274

Gnomad4 AFR AF: 0.227

Gnomad4 AMR AF: 0.0757

Gnomad4 ASJ AF: 0.137

Gnomad4 EAS AF: 0.366

Gnomad4 SAS AF: 0.114

Gnomad4 FIN AF: 0.159

Gnomad4 NFE AF: 0.0822

Gnomad4 OTH AF: 0.123

Alfa AF: 0.0941 Hom.: 1756

Bravo AF: 0.138

Asia WGS AF: 0.180 AC: 627 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	3.8
DANN	Benign	0.38

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1916141; hg19: chr2-57514841;