2-163461366-T-C

Variant names:

• chr2-163461366-T-C
• rs12476047

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 0.25 in 152,054 control chromosomes in the GnomAD database, including 5,179 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 0.25 (5179 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.30

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.358 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: 0.250 AC: 37950 AN: 151934 Hom.: 5175 Cov.: 32

Gnomad AFR AF: 0.146

Gnomad AMI AF: 0.434

Gnomad AMR AF: 0.365

Gnomad ASJ AF: 0.319

Gnomad EAS AF: 0.202

Gnomad SAS AF: 0.146

Gnomad FIN AF: 0.257

Gnomad MID AF: 0.402

Gnomad NFE AF: 0.289

Gnomad OTH AF: 0.284

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

GnomAD4 genome AF: 0.250 AC: 37988 AN: 152054 Hom.: 5179 Cov.: 32 AF XY: 0.249 AC XY: 18484 AN XY: 74324

Gnomad4 AFR AF: 0.146

Gnomad4 AMR AF: 0.366

Gnomad4 ASJ AF: 0.319

Gnomad4 EAS AF: 0.201

Gnomad4 SAS AF: 0.147

Gnomad4 FIN AF: 0.257

Gnomad4 NFE AF: 0.289

Gnomad4 OTH AF: 0.282

Alfa AF: 0.294 Hom.: 12172

Bravo AF: 0.262

Asia WGS AF: 0.153 AC: 532 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	12
DANN	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12476047; hg19: chr2-164317876;