rs7528615

Variant names:

• chr1-84267280-T-C
• rs7528615

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 0.287 in 152,024 control chromosomes in the GnomAD database, including 7,758 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 0.29 (7758 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.04

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.605 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: 0.288 AC: 43686 AN: 151906 Hom.: 7757 Cov.: 31

Gnomad AFR AF: 0.0828

Gnomad AMI AF: 0.330

Gnomad AMR AF: 0.317

Gnomad ASJ AF: 0.222

Gnomad EAS AF: 0.622

Gnomad SAS AF: 0.493

Gnomad FIN AF: 0.314

Gnomad MID AF: 0.209

Gnomad NFE AF: 0.365

Gnomad OTH AF: 0.268

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

GnomAD4 genome AF: 0.287 AC: 43681 AN: 152024 Hom.: 7758 Cov.: 31 AF XY: 0.290 AC XY: 21573 AN XY: 74302

Gnomad4 AFR AF: 0.0826

Gnomad4 AMR AF: 0.317

Gnomad4 ASJ AF: 0.222

Gnomad4 EAS AF: 0.623

Gnomad4 SAS AF: 0.494

Gnomad4 FIN AF: 0.314

Gnomad4 NFE AF: 0.365

Gnomad4 OTH AF: 0.269

Alfa AF: 0.345 Hom.: 13287

Bravo AF: 0.276

Asia WGS AF: 0.463 AC: 1611 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.18
DANN	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7528615; hg19: chr1-84732963; COSMIC: COSV59966922;