rs1529001

Variant names:

• chr7-52713630-C-T
• rs1529001

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 0.433 in 151,420 control chromosomes in the GnomAD database, including 15,332 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 0.43 (15332 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.277
• Publications: 1 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 (EAS) allele frequency at 95% confidence interval = 0.628 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: 0.433 AC: 65521 AN: 151302 Hom.: 15310 Cov.: 31

Gnomad AFR AF: 0.592

Gnomad AMI AF: 0.528

Gnomad AMR AF: 0.462

Gnomad ASJ AF: 0.414

Gnomad EAS AF: 0.646

Gnomad SAS AF: 0.400

Gnomad FIN AF: 0.373

Gnomad MID AF: 0.434

Gnomad NFE AF: 0.325

Gnomad OTH AF: 0.444

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

GnomAD4 genome AF: 0.433 AC: 65593 AN: 151420 Hom.: 15332 Cov.: 31 AF XY: 0.438 AC XY: 32382 AN XY: 73966

African (AFR) AF: 0.592 AC: 24386 AN: 41196

American (AMR) AF: 0.462 AC: 7041 AN: 15238

Ashkenazi Jewish (ASJ) AF: 0.414 AC: 1435 AN: 3468

East Asian (EAS) AF: 0.646 AC: 3272 AN: 5064

South Asian (SAS) AF: 0.400 AC: 1921 AN: 4806

European-Finnish (FIN) AF: 0.373 AC: 3910 AN: 10480

Middle Eastern (MID) AF: 0.439 AC: 129 AN: 294

European-Non Finnish (NFE) AF: 0.325 AC: 22085 AN: 67872

Other (OTH) AF: 0.447 AC: 938 AN: 2100

Alfa AF: 0.350 Hom.: 9353

Bravo AF: 0.452

Asia WGS AF: 0.500 AC: 1738 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	4.0
DANN	Benign	0.56
PhyloP100		0.28

Splicing

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

Other links and lift over

dbSNP: rs1529001; hg19: chr7-52781324;