rs7523360

Variant names:

• chr1-115028221-T-G
• rs7523360

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 0.423 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
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.291 AC: 12059 AN: 41506

American (AMR) AF: 0.405 AC: 6189 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.539 AC: 1871 AN: 3472

East Asian (EAS) AF: 0.497 AC: 2569 AN: 5168

South Asian (SAS) AF: 0.386 AC: 1860 AN: 4824

European-Finnish (FIN) AF: 0.400 AC: 4228 AN: 10572

Middle Eastern (MID) AF: 0.480 AC: 141 AN: 294

European-Non Finnish (NFE) AF: 0.500 AC: 33983 AN: 67976

Other (OTH) AF: 0.448 AC: 946 AN: 2110

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.16
DANN	Benign	0.38
PhyloP100		-0.79

Splicing

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

Other links and lift over

dbSNP: rs7523360; hg19: chr1-115570842;