rs1525303

Variant names:

• chr7-70965150-T-A
• rs1525303

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 0.538 in 151,922 control chromosomes in the GnomAD database, including 23,502 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 0.54 (23502 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.239
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.74).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.636 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: 0.539 AC: 81778 AN: 151804 Hom.: 23503 Cov.: 32

Gnomad AFR AF: 0.325

Gnomad AMI AF: 0.547

Gnomad AMR AF: 0.534

Gnomad ASJ AF: 0.646

Gnomad EAS AF: 0.654

Gnomad SAS AF: 0.591

Gnomad FIN AF: 0.759

Gnomad MID AF: 0.554

Gnomad NFE AF: 0.617

Gnomad OTH AF: 0.568

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

GnomAD4 genome AF: 0.538 AC: 81791 AN: 151922 Hom.: 23502 Cov.: 32 AF XY: 0.543 AC XY: 40329 AN XY: 74264

African (AFR) AF: 0.324 AC: 13423 AN: 41392

American (AMR) AF: 0.533 AC: 8144 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.646 AC: 2240 AN: 3470

East Asian (EAS) AF: 0.655 AC: 3366 AN: 5142

South Asian (SAS) AF: 0.593 AC: 2854 AN: 4816

European-Finnish (FIN) AF: 0.759 AC: 8010 AN: 10550

Middle Eastern (MID) AF: 0.541 AC: 158 AN: 292

European-Non Finnish (NFE) AF: 0.617 AC: 41902 AN: 67966

Other (OTH) AF: 0.566 AC: 1196 AN: 2114

Alfa AF: 0.584 Hom.: 3348

Bravo AF: 0.518

Asia WGS AF: 0.568 AC: 1980 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.74
CADD	Benign	11
DANN	Benign	0.89
PhyloP100		0.24

Splicing

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

Other links and lift over

dbSNP: rs1525303; hg19: chr7-70430136;