chr7-34900272-T-C

Variant names:

• chr7-34900272-T-C
• rs1859409

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 0.619 in 152,024 control chromosomes in the GnomAD database, including 29,591 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 0.62 (29591 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.371
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.785 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.620 AC: 94113 AN: 151906 Hom.: 29566 Cov.: 32

Gnomad AFR AF: 0.545

Gnomad AMI AF: 0.620

Gnomad AMR AF: 0.539

Gnomad ASJ AF: 0.533

Gnomad EAS AF: 0.769

Gnomad SAS AF: 0.806

Gnomad FIN AF: 0.680

Gnomad MID AF: 0.592

Gnomad NFE AF: 0.654

Gnomad OTH AF: 0.594

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

GnomAD4 genome AF: 0.619 AC: 94177 AN: 152024 Hom.: 29591 Cov.: 32 AF XY: 0.624 AC XY: 46370 AN XY: 74320

African (AFR) AF: 0.545 AC: 22585 AN: 41456

American (AMR) AF: 0.539 AC: 8234 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.533 AC: 1846 AN: 3466

East Asian (EAS) AF: 0.769 AC: 3965 AN: 5156

South Asian (SAS) AF: 0.807 AC: 3886 AN: 4818

European-Finnish (FIN) AF: 0.680 AC: 7200 AN: 10582

Middle Eastern (MID) AF: 0.602 AC: 177 AN: 294

European-Non Finnish (NFE) AF: 0.654 AC: 44457 AN: 67954

Other (OTH) AF: 0.599 AC: 1263 AN: 2108

Alfa AF: 0.636 Hom.: 51136

Bravo AF: 0.602

Asia WGS AF: 0.785 AC: 2725 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.6
DANN	Benign	0.84
PhyloP100		0.37

Splicing

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

Other links and lift over

dbSNP: rs1859409; hg19: chr7-34939884;