rs1522596

Variant names:

• chr7-150538695-A-G
• rs1522596

Your query was ambiguous. Multiple possible variants found:

• chr7-150538695-A-G
• chr7-150538695-A-T

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 0.47 in 152,090 control chromosomes in the GnomAD database, including 16,998 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 0.47 (16998 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.218
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.495 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: 0.470 AC: 71495 AN: 151972 Hom.: 16985 Cov.: 33

Gnomad AFR AF: 0.456

Gnomad AMI AF: 0.515

Gnomad AMR AF: 0.504

Gnomad ASJ AF: 0.499

Gnomad EAS AF: 0.489

Gnomad SAS AF: 0.469

Gnomad FIN AF: 0.580

Gnomad MID AF: 0.437

Gnomad NFE AF: 0.453

Gnomad OTH AF: 0.421

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

GnomAD4 genome AF: 0.470 AC: 71553 AN: 152090 Hom.: 16998 Cov.: 33 AF XY: 0.477 AC XY: 35420 AN XY: 74332

African (AFR) AF: 0.456 AC: 18901 AN: 41484

American (AMR) AF: 0.504 AC: 7704 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.499 AC: 1731 AN: 3470

East Asian (EAS) AF: 0.490 AC: 2535 AN: 5176

South Asian (SAS) AF: 0.470 AC: 2265 AN: 4824

European-Finnish (FIN) AF: 0.580 AC: 6127 AN: 10566

Middle Eastern (MID) AF: 0.422 AC: 124 AN: 294

European-Non Finnish (NFE) AF: 0.453 AC: 30799 AN: 67972

Other (OTH) AF: 0.425 AC: 898 AN: 2114

Alfa AF: 0.458 Hom.: 45580

Bravo AF: 0.466

Asia WGS AF: 0.474 AC: 1647 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	7.0
DANN	Benign	0.68
PhyloP100		0.22

Splicing

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

Other links and lift over

dbSNP: rs1522596; hg19: chr7-150235783;