2-176908534-C-G

Variant names:

• chr2-176908534-C-G
• rs4894215

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.449 in 152,034 control chromosomes in the GnomAD database, including 16,480 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 0.45 (16480 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.97

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.32).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.933 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: 0.449 AC: 68151 AN: 151916 Hom.: 16462 Cov.: 32

Gnomad AFR AF: 0.361

Gnomad AMI AF: 0.320

Gnomad AMR AF: 0.550

Gnomad ASJ AF: 0.411

Gnomad EAS AF: 0.954

Gnomad SAS AF: 0.652

Gnomad FIN AF: 0.476

Gnomad MID AF: 0.472

Gnomad NFE AF: 0.426

Gnomad OTH AF: 0.424

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

GnomAD4 genome AF: 0.449 AC: 68220 AN: 152034 Hom.: 16480 Cov.: 32 AF XY: 0.457 AC XY: 33954 AN XY: 74298

Gnomad4 AFR AF: 0.362

Gnomad4 AMR AF: 0.551

Gnomad4 ASJ AF: 0.411

Gnomad4 EAS AF: 0.955

Gnomad4 SAS AF: 0.651

Gnomad4 FIN AF: 0.476

Gnomad4 NFE AF: 0.426

Gnomad4 OTH AF: 0.424

Alfa AF: 0.326 Hom.: 902

Bravo AF: 0.447

Asia WGS AF: 0.727 AC: 2530 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.32
CADD	Benign	19
DANN	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4894215; hg19: chr2-177773262;