chr2-192871656-C-T

Position:

• chr2-192871656-C-T

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 0.415 in 151,486 control chromosomes in the GnomAD database, including 13,395 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 0.41 (13395 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00700

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.38).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.507 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.414 AC: 62742 AN: 151368 Hom.: 13380 Cov.: 33

Gnomad AFR AF: 0.513

Gnomad AMI AF: 0.201

Gnomad AMR AF: 0.377

Gnomad ASJ AF: 0.415

Gnomad EAS AF: 0.477

Gnomad SAS AF: 0.451

Gnomad FIN AF: 0.352

Gnomad MID AF: 0.452

Gnomad NFE AF: 0.367

Gnomad OTH AF: 0.428

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

GnomAD4 genome AF: 0.415 AC: 62798 AN: 151486 Hom.: 13395 Cov.: 33 AF XY: 0.412 AC XY: 30508 AN XY: 74008

Gnomad4 AFR AF: 0.513

Gnomad4 AMR AF: 0.377

Gnomad4 ASJ AF: 0.415

Gnomad4 EAS AF: 0.477

Gnomad4 SAS AF: 0.452

Gnomad4 FIN AF: 0.352

Gnomad4 NFE AF: 0.367

Gnomad4 OTH AF: 0.434

Alfa AF: 0.385 Hom.: 5474

Bravo AF: 0.417

Asia WGS AF: 0.515 AC: 1785 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.38
CADD	Benign	10
DANN	Benign	0.85

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1373900; hg19: chr2-193736382;