2-105722179-G-C

Variant names:

• chr2-105722179-G-C
• rs955798

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 0.365 in 151,974 control chromosomes in the GnomAD database, including 10,665 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 0.36 (10665 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.165

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.486 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: 0.365 AC: 55395 AN: 151856 Hom.: 10649 Cov.: 32

Gnomad AFR AF: 0.492

Gnomad AMI AF: 0.314

Gnomad AMR AF: 0.359

Gnomad ASJ AF: 0.260

Gnomad EAS AF: 0.403

Gnomad SAS AF: 0.316

Gnomad FIN AF: 0.359

Gnomad MID AF: 0.259

Gnomad NFE AF: 0.298

Gnomad OTH AF: 0.342

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

GnomAD4 genome AF: 0.365 AC: 55456 AN: 151974 Hom.: 10665 Cov.: 32 AF XY: 0.366 AC XY: 27213 AN XY: 74272

Gnomad4 AFR AF: 0.492

Gnomad4 AMR AF: 0.359

Gnomad4 ASJ AF: 0.260

Gnomad4 EAS AF: 0.403

Gnomad4 SAS AF: 0.314

Gnomad4 FIN AF: 0.359

Gnomad4 NFE AF: 0.298

Gnomad4 OTH AF: 0.342

Alfa AF: 0.175 Hom.: 352

Bravo AF: 0.371

Asia WGS AF: 0.359 AC: 1248 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.7
DANN	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs955798; hg19: chr2-106338636;