2-7192804-C-T

Variant names:

• chr2-7192804-C-T
• rs1404841

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 0.507 in 151,982 control chromosomes in the GnomAD database, including 21,752 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 (21752 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.564
• Publications: 5 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• 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: 0.507 AC: 77024 AN: 151864 Hom.: 21745 Cov.: 32

Gnomad AFR AF: 0.238

Gnomad AMI AF: 0.491

Gnomad AMR AF: 0.627

Gnomad ASJ AF: 0.606

Gnomad EAS AF: 0.443

Gnomad SAS AF: 0.531

Gnomad FIN AF: 0.571

Gnomad MID AF: 0.570

Gnomad NFE AF: 0.631

Gnomad OTH AF: 0.533

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

GnomAD4 genome AF: 0.507 AC: 77040 AN: 151982 Hom.: 21752 Cov.: 32 AF XY: 0.507 AC XY: 37691 AN XY: 74288

African (AFR) AF: 0.238 AC: 9861 AN: 41410

American (AMR) AF: 0.628 AC: 9597 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.606 AC: 2099 AN: 3464

East Asian (EAS) AF: 0.443 AC: 2289 AN: 5172

South Asian (SAS) AF: 0.529 AC: 2545 AN: 4808

European-Finnish (FIN) AF: 0.571 AC: 6016 AN: 10530

Middle Eastern (MID) AF: 0.568 AC: 167 AN: 294

European-Non Finnish (NFE) AF: 0.631 AC: 42889 AN: 67988

Other (OTH) AF: 0.535 AC: 1130 AN: 2114

Alfa AF: 0.496 Hom.: 2793

Bravo AF: 0.498

Asia WGS AF: 0.501 AC: 1740 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.030
DANN	Benign	0.19
PhyloP100		-0.56

Splicing

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

Other links and lift over

dbSNP: rs1404841; hg19: chr2-7332935;