rs1522596

Positions:

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

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.456

Gnomad4 AMR AF: 0.504

Gnomad4 ASJ AF: 0.499

Gnomad4 EAS AF: 0.490

Gnomad4 SAS AF: 0.470

Gnomad4 FIN AF: 0.580

Gnomad4 NFE AF: 0.453

Gnomad4 OTH AF: 0.425

Alfa AF: 0.455 Hom.: 27687

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1522596; hg19: chr7-150235783;