7-15025378-T-C

Variant names:

• chr7-15025378-T-C
• rs4719433

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 0.555 in 151,936 control chromosomes in the GnomAD database, including 23,749 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 0.55 (23749 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00500
• Publications: 11 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.662 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: 0.555 AC: 84243 AN: 151820 Hom.: 23735 Cov.: 31

Gnomad AFR AF: 0.608

Gnomad AMI AF: 0.460

Gnomad AMR AF: 0.486

Gnomad ASJ AF: 0.554

Gnomad EAS AF: 0.681

Gnomad SAS AF: 0.622

Gnomad FIN AF: 0.440

Gnomad MID AF: 0.506

Gnomad NFE AF: 0.543

Gnomad OTH AF: 0.542

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

GnomAD4 genome AF: 0.555 AC: 84310 AN: 151936 Hom.: 23749 Cov.: 31 AF XY: 0.550 AC XY: 40866 AN XY: 74268

African (AFR) AF: 0.608 AC: 25178 AN: 41410

American (AMR) AF: 0.486 AC: 7426 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.554 AC: 1925 AN: 3472

East Asian (EAS) AF: 0.681 AC: 3506 AN: 5148

South Asian (SAS) AF: 0.622 AC: 3002 AN: 4824

European-Finnish (FIN) AF: 0.440 AC: 4646 AN: 10568

Middle Eastern (MID) AF: 0.493 AC: 145 AN: 294

European-Non Finnish (NFE) AF: 0.543 AC: 36906 AN: 67926

Other (OTH) AF: 0.547 AC: 1157 AN: 2114

Alfa AF: 0.571 Hom.: 6118

Bravo AF: 0.557

Asia WGS AF: 0.645 AC: 2241 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	4.3
DANN	Benign	0.72
PhyloP100		-0.0050

Splicing

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

Other links and lift over

dbSNP: rs4719433; hg19: chr7-15065003;