5-17362696-C-T

Variant names:

• chr5-17362696-C-T
• rs2036848

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 0.372 in 151,760 control chromosomes in the GnomAD database, including 10,697 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 0.37 (10697 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.35

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 (SAS) allele frequency at 95% confidence interval = 0.474 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: 0.373 AC: 56491 AN: 151642 Hom.: 10698 Cov.: 31

Gnomad AFR AF: 0.353

Gnomad AMI AF: 0.272

Gnomad AMR AF: 0.270

Gnomad ASJ AF: 0.365

Gnomad EAS AF: 0.405

Gnomad SAS AF: 0.492

Gnomad FIN AF: 0.421

Gnomad MID AF: 0.519

Gnomad NFE AF: 0.390

Gnomad OTH AF: 0.369

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

GnomAD4 genome AF: 0.372 AC: 56492 AN: 151760 Hom.: 10697 Cov.: 31 AF XY: 0.372 AC XY: 27606 AN XY: 74134

Gnomad4 AFR AF: 0.353

Gnomad4 AMR AF: 0.270

Gnomad4 ASJ AF: 0.365

Gnomad4 EAS AF: 0.404

Gnomad4 SAS AF: 0.490

Gnomad4 FIN AF: 0.421

Gnomad4 NFE AF: 0.390

Gnomad4 OTH AF: 0.367

Alfa AF: 0.322 Hom.: 1530

Bravo AF: 0.358

Asia WGS AF: 0.423 AC: 1471 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	1.3
DANN	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2036848; hg19: chr5-17362805; COSMIC: COSV59181217;