7-15025987-A-T

Variant names:

• chr7-15025987-A-T
• rs1558318

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.551 in 151,982 control chromosomes in the GnomAD database, including 23,425 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 (23425 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.214
• Publications: 9 publications found

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.4).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.661 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: 0.551 AC: 83717 AN: 151864 Hom.: 23411 Cov.: 32

Gnomad AFR AF: 0.601

Gnomad AMI AF: 0.459

Gnomad AMR AF: 0.484

Gnomad ASJ AF: 0.552

Gnomad EAS AF: 0.680

Gnomad SAS AF: 0.613

Gnomad FIN AF: 0.437

Gnomad MID AF: 0.509

Gnomad NFE AF: 0.541

Gnomad OTH AF: 0.541

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

GnomAD4 genome AF: 0.551 AC: 83785 AN: 151982 Hom.: 23425 Cov.: 32 AF XY: 0.546 AC XY: 40570 AN XY: 74272

African (AFR) AF: 0.601 AC: 24909 AN: 41450

American (AMR) AF: 0.484 AC: 7385 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.552 AC: 1917 AN: 3470

East Asian (EAS) AF: 0.680 AC: 3511 AN: 5162

South Asian (SAS) AF: 0.614 AC: 2963 AN: 4828

European-Finnish (FIN) AF: 0.437 AC: 4604 AN: 10546

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

European-Non Finnish (NFE) AF: 0.541 AC: 36783 AN: 67960

Other (OTH) AF: 0.547 AC: 1151 AN: 2106

Alfa AF: 0.548 Hom.: 2844

Bravo AF: 0.554

Asia WGS AF: 0.641 AC: 2227 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.40
CADD	Benign	13
DANN	Benign	0.77
PhyloP100		0.21

Splicing

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

Other links and lift over

dbSNP: rs1558318; hg19: chr7-15065612;