chr2-190858993-C-T

Variant names:

• chr2-190858993-C-T
• rs6741418

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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;