chr7-15025842-C-T

Variant names:

• chr7-15025842-C-T
• rs1974620

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 0.553 in 151,972 control chromosomes in the GnomAD database, including 23,545 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 (23545 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.729
• Publications: 18 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.661 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.553 AC: 83945 AN: 151854 Hom.: 23532 Cov.: 32

Gnomad AFR AF: 0.601

Gnomad AMI AF: 0.460

Gnomad AMR AF: 0.485

Gnomad ASJ AF: 0.555

Gnomad EAS AF: 0.680

Gnomad SAS AF: 0.615

Gnomad FIN AF: 0.440

Gnomad MID AF: 0.509

Gnomad NFE AF: 0.543

Gnomad OTH AF: 0.541

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

GnomAD4 genome AF: 0.553 AC: 84011 AN: 151972 Hom.: 23545 Cov.: 32 AF XY: 0.548 AC XY: 40700 AN XY: 74262

African (AFR) AF: 0.601 AC: 24919 AN: 41444

American (AMR) AF: 0.485 AC: 7404 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.555 AC: 1925 AN: 3470

East Asian (EAS) AF: 0.680 AC: 3509 AN: 5160

South Asian (SAS) AF: 0.616 AC: 2968 AN: 4822

European-Finnish (FIN) AF: 0.440 AC: 4641 AN: 10536

Middle Eastern (MID) AF: 0.497 AC: 146 AN: 294

European-Non Finnish (NFE) AF: 0.543 AC: 36928 AN: 67966

Other (OTH) AF: 0.547 AC: 1152 AN: 2106

Alfa AF: 0.550 Hom.: 49809

Bravo AF: 0.555

Asia WGS AF: 0.641 AC: 2227 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	0.060
DANN	Benign	0.73
PhyloP100		-0.73

Splicing

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

Other links and lift over

dbSNP: rs1974620; hg19: chr7-15065467;