2-190858993-C-T

Position:

• chr2-190858993-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 0.107 in 152,142 control chromosomes in the GnomAD database, including 1,162 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 0.11 (1162 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.03

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.41).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.154 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.107 AC: 16274 AN: 152024 Hom.: 1161 Cov.: 32

Gnomad AFR AF: 0.0293

Gnomad AMI AF: 0.259

Gnomad AMR AF: 0.115

Gnomad ASJ AF: 0.186

Gnomad EAS AF: 0.000963

Gnomad SAS AF: 0.0467

Gnomad FIN AF: 0.115

Gnomad MID AF: 0.158

Gnomad NFE AF: 0.157

Gnomad OTH AF: 0.130

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

GnomAD4 genome AF: 0.107 AC: 16277 AN: 152142 Hom.: 1162 Cov.: 32 AF XY: 0.105 AC XY: 7772 AN XY: 74368

Gnomad4 AFR AF: 0.0293

Gnomad4 AMR AF: 0.114

Gnomad4 ASJ AF: 0.186

Gnomad4 EAS AF: 0.000965

Gnomad4 SAS AF: 0.0461

Gnomad4 FIN AF: 0.115

Gnomad4 NFE AF: 0.157

Gnomad4 OTH AF: 0.129

Alfa AF: 0.156 Hom.: 1747

Bravo AF: 0.107

Asia WGS AF: 0.0240 AC: 85 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.41
CADD	Benign	17
DANN	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6741418; hg19: chr2-191723719;