rs2985159

Positions:

• chr13-37602352-T-G

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 0.294 in 151,892 control chromosomes in the GnomAD database, including 6,989 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 (6989 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.474

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.348 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.294 AC: 44639 AN: 151774 Hom.: 6979 Cov.: 32

Gnomad AFR AF: 0.206

Gnomad AMI AF: 0.270

Gnomad AMR AF: 0.290

Gnomad ASJ AF: 0.492

Gnomad EAS AF: 0.162

Gnomad SAS AF: 0.334

Gnomad FIN AF: 0.253

Gnomad MID AF: 0.294

Gnomad NFE AF: 0.352

Gnomad OTH AF: 0.311

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

GnomAD4 genome AF: 0.294 AC: 44667 AN: 151892 Hom.: 6989 Cov.: 32 AF XY: 0.285 AC XY: 21189 AN XY: 74254

Gnomad4 AFR AF: 0.206

Gnomad4 AMR AF: 0.290

Gnomad4 ASJ AF: 0.492

Gnomad4 EAS AF: 0.162

Gnomad4 SAS AF: 0.334

Gnomad4 FIN AF: 0.253

Gnomad4 NFE AF: 0.352

Gnomad4 OTH AF: 0.313

Alfa AF: 0.339 Hom.: 4436

Bravo AF: 0.295

Asia WGS AF: 0.258 AC: 897 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	13
DANN	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2985159; hg19: chr13-38176489; COSMIC: COSV65713182;