1-152573517-C-G

Variant names:

• chr1-152573517-C-G
• rs10888502

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 0.43 in 150,200 control chromosomes in the GnomAD database, including 14,476 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 (14476 hom., cov: 27)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.297
• Publications: 5 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.554 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: 0.430 AC: 64566 AN: 150084 Hom.: 14454 Cov.: 27

Gnomad AFR AF: 0.561

Gnomad AMI AF: 0.334

Gnomad AMR AF: 0.367

Gnomad ASJ AF: 0.238

Gnomad EAS AF: 0.360

Gnomad SAS AF: 0.312

Gnomad FIN AF: 0.409

Gnomad MID AF: 0.458

Gnomad NFE AF: 0.394

Gnomad OTH AF: 0.420

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

GnomAD4 genome AF: 0.430 AC: 64620 AN: 150200 Hom.: 14476 Cov.: 27 AF XY: 0.428 AC XY: 31328 AN XY: 73246

African (AFR) AF: 0.561 AC: 22889 AN: 40832

American (AMR) AF: 0.366 AC: 5392 AN: 14738

Ashkenazi Jewish (ASJ) AF: 0.238 AC: 824 AN: 3462

East Asian (EAS) AF: 0.361 AC: 1825 AN: 5054

South Asian (SAS) AF: 0.311 AC: 1481 AN: 4760

European-Finnish (FIN) AF: 0.409 AC: 4219 AN: 10310

Middle Eastern (MID) AF: 0.462 AC: 133 AN: 288

European-Non Finnish (NFE) AF: 0.394 AC: 26675 AN: 67762

Other (OTH) AF: 0.421 AC: 878 AN: 2084

Alfa AF: 0.409 Hom.: 1733

Bravo AF: 0.429

Asia WGS AF: 0.362 AC: 1260 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.7
DANN	Benign	0.52
PhyloP100		-0.30

Splicing

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

Other links and lift over

dbSNP: rs10888502; hg19: chr1-152545993;