2-57176051-A-G

Position:

• chr2-57176051-A-G

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 0.0435 in 152,146 control chromosomes in the GnomAD database, including 566 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 0.043 (566 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.771

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.389 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.57176051A>G		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0436 AC: 6623 AN: 152028 Hom.: 568 Cov.: 32

Gnomad AFR AF: 0.0818

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0191

Gnomad ASJ AF: 0.0519

Gnomad EAS AF: 0.404

Gnomad SAS AF: 0.0321

Gnomad FIN AF: 0.00725

Gnomad MID AF: 0.0701

Gnomad NFE AF: 0.00493

Gnomad OTH AF: 0.0471

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

GnomAD4 genome AF: 0.0435 AC: 6613 AN: 152146 Hom.: 566 Cov.: 32 AF XY: 0.0457 AC XY: 3399 AN XY: 74364

Gnomad4 AFR AF: 0.0816

Gnomad4 AMR AF: 0.0191

Gnomad4 ASJ AF: 0.0519

Gnomad4 EAS AF: 0.403

Gnomad4 SAS AF: 0.0319

Gnomad4 FIN AF: 0.00725

Gnomad4 NFE AF: 0.00493

Gnomad4 OTH AF: 0.0461

Alfa AF: 0.0230 Hom.: 28

Bravo AF: 0.0499

Asia WGS AF: 0.161 AC: 559 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.034
DANN	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs8179620; hg19: chr2-57403186;