17-13636487-T-C

Variant names:

• chr17-13636487-T-C
• rs10521232

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 0.348 in 151,966 control chromosomes in the GnomAD database, including 9,460 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 0.35 (9460 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.286
• Publications: 8 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.39 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: 0.349 AC: 52929 AN: 151848 Hom.: 9462 Cov.: 33

Gnomad AFR AF: 0.319

Gnomad AMI AF: 0.334

Gnomad AMR AF: 0.275

Gnomad ASJ AF: 0.408

Gnomad EAS AF: 0.229

Gnomad SAS AF: 0.373

Gnomad FIN AF: 0.301

Gnomad MID AF: 0.468

Gnomad NFE AF: 0.394

Gnomad OTH AF: 0.354

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

GnomAD4 genome AF: 0.348 AC: 52936 AN: 151966 Hom.: 9460 Cov.: 33 AF XY: 0.342 AC XY: 25423 AN XY: 74286

African (AFR) AF: 0.319 AC: 13230 AN: 41468

American (AMR) AF: 0.275 AC: 4189 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.408 AC: 1413 AN: 3466

East Asian (EAS) AF: 0.229 AC: 1184 AN: 5180

South Asian (SAS) AF: 0.372 AC: 1792 AN: 4818

European-Finnish (FIN) AF: 0.301 AC: 3160 AN: 10496

Middle Eastern (MID) AF: 0.438 AC: 128 AN: 292

European-Non Finnish (NFE) AF: 0.394 AC: 26794 AN: 67964

Other (OTH) AF: 0.351 AC: 741 AN: 2110

Alfa AF: 0.383 Hom.: 23276

Bravo AF: 0.343

Asia WGS AF: 0.283 AC: 983 AN: 3464

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.2
DANN	Benign	0.68
PhyloP100		-0.29

Splicing

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

Other links and lift over

dbSNP: rs10521232; hg19: chr17-13539804; COSMIC: COSV69372551;