rs7523360

Variant names:

• chr1-115028221-T-G
• rs7523360

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 0.423 in 152,120 control chromosomes in the GnomAD database, including 14,322 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 0.42 (14322 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.790

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (NFE) 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: 0.423 AC: 64259 AN: 152002 Hom.: 14323 Cov.: 32

Gnomad AFR AF: 0.291

Gnomad AMI AF: 0.468

Gnomad AMR AF: 0.404

Gnomad ASJ AF: 0.539

Gnomad EAS AF: 0.498

Gnomad SAS AF: 0.387

Gnomad FIN AF: 0.400

Gnomad MID AF: 0.484

Gnomad NFE AF: 0.500

Gnomad OTH AF: 0.452

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

GnomAD4 genome AF: 0.423 AC: 64273 AN: 152120 Hom.: 14322 Cov.: 32 AF XY: 0.418 AC XY: 31049 AN XY: 74364

Gnomad4 AFR AF: 0.291

Gnomad4 AMR AF: 0.405

Gnomad4 ASJ AF: 0.539

Gnomad4 EAS AF: 0.497

Gnomad4 SAS AF: 0.386

Gnomad4 FIN AF: 0.400

Gnomad4 NFE AF: 0.500

Gnomad4 OTH AF: 0.448

Alfa AF: 0.455 Hom.: 2791

Bravo AF: 0.421

Asia WGS AF: 0.406 AC: 1411 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.16
DANN	Benign	0.38

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7523360; hg19: chr1-115570842;