rs1558317

Variant names:

• chr7-15025939-T-A
• rs1558317

Your query was ambiguous. Multiple possible variants found:

• chr7-15025939-T-A
• chr7-15025939-T-G

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 0.552 in 152,010 control chromosomes in the GnomAD database, including 23,454 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 (23454 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0430
• Publications: 9 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 = 0.661 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: 0.552 AC: 83781 AN: 151892 Hom.: 23440 Cov.: 32

Gnomad AFR AF: 0.601

Gnomad AMI AF: 0.461

Gnomad AMR AF: 0.484

Gnomad ASJ AF: 0.557

Gnomad EAS AF: 0.680

Gnomad SAS AF: 0.613

Gnomad FIN AF: 0.438

Gnomad MID AF: 0.509

Gnomad NFE AF: 0.541

Gnomad OTH AF: 0.540

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

GnomAD4 genome AF: 0.552 AC: 83848 AN: 152010 Hom.: 23454 Cov.: 32 AF XY: 0.547 AC XY: 40600 AN XY: 74262

African (AFR) AF: 0.601 AC: 24922 AN: 41454

American (AMR) AF: 0.484 AC: 7396 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.557 AC: 1933 AN: 3468

East Asian (EAS) AF: 0.679 AC: 3507 AN: 5162

South Asian (SAS) AF: 0.614 AC: 2963 AN: 4824

European-Finnish (FIN) AF: 0.438 AC: 4614 AN: 10542

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

European-Non Finnish (NFE) AF: 0.541 AC: 36798 AN: 67974

Other (OTH) AF: 0.546 AC: 1151 AN: 2108

Alfa AF: 0.548 Hom.: 2849

Bravo AF: 0.554

Asia WGS AF: 0.640 AC: 2225 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	2.3
DANN	Benign	0.59
PhyloP100		-0.043

Splicing

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

Other links and lift over

dbSNP: rs1558317; hg19: chr7-15065564;