chr2-7192667-C-T

Variant names:

• chr2-7192667-C-T
• rs1404843

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 6 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.239 AC: 9834 AN: 41172

American (AMR) AF: 0.629 AC: 9547 AN: 15170

Ashkenazi Jewish (ASJ) AF: 0.605 AC: 2099 AN: 3470

East Asian (EAS) AF: 0.445 AC: 2284 AN: 5134

South Asian (SAS) AF: 0.531 AC: 2543 AN: 4792

European-Finnish (FIN) AF: 0.570 AC: 5940 AN: 10412

Middle Eastern (MID) AF: 0.572 AC: 167 AN: 292

European-Non Finnish (NFE) AF: 0.631 AC: 42839 AN: 67906

Other (OTH) AF: 0.536 AC: 1126 AN: 2100

Alfa AF: 0.559 Hom.: 3601

Bravo AF: 0.498

Asia WGS AF: 0.501 AC: 1741 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.4
DANN	Benign	0.11
PhyloP100		-0.28

Splicing

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

Other links and lift over

dbSNP: rs1404843; hg19: chr2-7332798;