rs10496057

Variant names:

• chr2-56977695-G-A
• rs10496057

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 0.0468 in 152,128 control chromosomes in the GnomAD database, including 449 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 0.047 (449 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0320

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.141 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: 0.0467 AC: 7097 AN: 152010 Hom.: 446 Cov.: 32

Gnomad AFR AF: 0.144

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0285

Gnomad ASJ AF: 0.00866

Gnomad EAS AF: 0.0177

Gnomad SAS AF: 0.00186

Gnomad FIN AF: 0.00567

Gnomad MID AF: 0.0158

Gnomad NFE AF: 0.00647

Gnomad OTH AF: 0.0402

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

GnomAD4 genome AF: 0.0468 AC: 7117 AN: 152128 Hom.: 449 Cov.: 32 AF XY: 0.0456 AC XY: 3392 AN XY: 74370

Gnomad4 AFR AF: 0.144

Gnomad4 AMR AF: 0.0284

Gnomad4 ASJ AF: 0.00866

Gnomad4 EAS AF: 0.0177

Gnomad4 SAS AF: 0.00187

Gnomad4 FIN AF: 0.00567

Gnomad4 NFE AF: 0.00647

Gnomad4 OTH AF: 0.0398

Alfa AF: 0.0312 Hom.: 35

Bravo AF: 0.0526

Asia WGS AF: 0.0220 AC: 77 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.4
DANN	Benign	0.28

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10496057; hg19: chr2-57204830;