2-7192667-C-T

Variant names:

• chr2-7192667-C-T
• rs1404843

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;