rs17375349

Positions:

• chr3-137086251-C-A
• chr3-137086251-C-T

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 0.219 in 152,146 control chromosomes in the GnomAD database, including 3,761 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 0.22 (3761 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.38

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.251 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.219 AC: 33362 AN: 152028 Hom.: 3760 Cov.: 32

Gnomad AFR AF: 0.182

Gnomad AMI AF: 0.224

Gnomad AMR AF: 0.183

Gnomad ASJ AF: 0.240

Gnomad EAS AF: 0.123

Gnomad SAS AF: 0.158

Gnomad FIN AF: 0.267

Gnomad MID AF: 0.237

Gnomad NFE AF: 0.255

Gnomad OTH AF: 0.189

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

GnomAD4 genome AF: 0.219 AC: 33373 AN: 152146 Hom.: 3761 Cov.: 32 AF XY: 0.218 AC XY: 16224 AN XY: 74368

Gnomad4 AFR AF: 0.182

Gnomad4 AMR AF: 0.183

Gnomad4 ASJ AF: 0.240

Gnomad4 EAS AF: 0.124

Gnomad4 SAS AF: 0.159

Gnomad4 FIN AF: 0.267

Gnomad4 NFE AF: 0.254

Gnomad4 OTH AF: 0.187

Alfa AF: 0.238 Hom.: 6842

Bravo AF: 0.210

Asia WGS AF: 0.131 AC: 460 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.023
DANN	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17375349; hg19: chr3-136805093;