chr2-7192667-C-T

Position:

• chr2-7192667-C-T

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 0.508 in 151,350 control chromosomes in the GnomAD database, including 21,701 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 0.51 (21701 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.283

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.626 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: 0.508 AC: 76808 AN: 151230 Hom.: 21694 Cov.: 30

Gnomad AFR AF: 0.239

Gnomad AMI AF: 0.493

Gnomad AMR AF: 0.629

Gnomad ASJ AF: 0.605

Gnomad EAS AF: 0.446

Gnomad SAS AF: 0.532

Gnomad FIN AF: 0.570

Gnomad MID AF: 0.573

Gnomad NFE AF: 0.631

Gnomad OTH AF: 0.535

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

GnomAD4 genome AF: 0.508 AC: 76824 AN: 151350 Hom.: 21701 Cov.: 30 AF XY: 0.508 AC XY: 37546 AN XY: 73880

Gnomad4 AFR AF: 0.239

Gnomad4 AMR AF: 0.629

Gnomad4 ASJ AF: 0.605

Gnomad4 EAS AF: 0.445

Gnomad4 SAS AF: 0.531

Gnomad4 FIN AF: 0.570

Gnomad4 NFE AF: 0.631

Gnomad4 OTH AF: 0.536

Alfa AF: 0.570 Hom.: 3576

Bravo AF: 0.498

Asia WGS AF: 0.501 AC: 1741 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.4
DANN	Benign	0.11

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1404843; hg19: chr2-7332798;