chr2-191495052-C-T

Variant names:

• chr2-191495052-C-T
• rs7559874

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 0.686 in 152,012 control chromosomes in the GnomAD database, including 38,635 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 0.69 (38635 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.358

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.843 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: 0.686 AC: 104224 AN: 151894 Hom.: 38637 Cov.: 31

Gnomad AFR AF: 0.422

Gnomad AMI AF: 0.870

Gnomad AMR AF: 0.645

Gnomad ASJ AF: 0.769

Gnomad EAS AF: 0.382

Gnomad SAS AF: 0.698

Gnomad FIN AF: 0.827

Gnomad MID AF: 0.752

Gnomad NFE AF: 0.849

Gnomad OTH AF: 0.691

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

GnomAD4 genome AF: 0.686 AC: 104236 AN: 152012 Hom.: 38635 Cov.: 31 AF XY: 0.681 AC XY: 50599 AN XY: 74306

Gnomad4 AFR AF: 0.421

Gnomad4 AMR AF: 0.644

Gnomad4 ASJ AF: 0.769

Gnomad4 EAS AF: 0.384

Gnomad4 SAS AF: 0.699

Gnomad4 FIN AF: 0.827

Gnomad4 NFE AF: 0.849

Gnomad4 OTH AF: 0.689

Alfa AF: 0.796 Hom.: 22657

Bravo AF: 0.655

Asia WGS AF: 0.574 AC: 2000 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	1.0
DANN	Benign	0.83

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7559874; hg19: chr2-192359778;