2-192469177-C-T

Variant names:

• chr2-192469177-C-T
• rs1385351

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 0.761 in 151,962 control chromosomes in the GnomAD database, including 44,554 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 0.76 (44554 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.19

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.57).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.825 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: 0.761 AC: 115497 AN: 151842 Hom.: 44520 Cov.: 32

Gnomad AFR AF: 0.624

Gnomad AMI AF: 0.819

Gnomad AMR AF: 0.780

Gnomad ASJ AF: 0.741

Gnomad EAS AF: 0.778

Gnomad SAS AF: 0.769

Gnomad FIN AF: 0.816

Gnomad MID AF: 0.651

Gnomad NFE AF: 0.831

Gnomad OTH AF: 0.725

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

GnomAD4 genome AF: 0.761 AC: 115582 AN: 151962 Hom.: 44554 Cov.: 32 AF XY: 0.761 AC XY: 56530 AN XY: 74252

Gnomad4 AFR AF: 0.624

Gnomad4 AMR AF: 0.780

Gnomad4 ASJ AF: 0.741

Gnomad4 EAS AF: 0.778

Gnomad4 SAS AF: 0.770

Gnomad4 FIN AF: 0.816

Gnomad4 NFE AF: 0.831

Gnomad4 OTH AF: 0.727

Alfa AF: 0.813 Hom.: 56009

Bravo AF: 0.751

Asia WGS AF: 0.729 AC: 2529 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.57
CADD	Benign	12
DANN	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1385351; hg19: chr2-193333903;