rs17374749

Variant names:

• chr3-137049168-G-A
• rs17374749

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 0.265 in 152,140 control chromosomes in the GnomAD database, including 6,128 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 0.26 (6128 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.875

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.408 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: 0.265 AC: 40257 AN: 152022 Hom.: 6119 Cov.: 32

Gnomad AFR AF: 0.413

Gnomad AMI AF: 0.220

Gnomad AMR AF: 0.211

Gnomad ASJ AF: 0.223

Gnomad EAS AF: 0.119

Gnomad SAS AF: 0.147

Gnomad FIN AF: 0.141

Gnomad MID AF: 0.263

Gnomad NFE AF: 0.229

Gnomad OTH AF: 0.240

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

GnomAD4 genome AF: 0.265 AC: 40287 AN: 152140 Hom.: 6128 Cov.: 32 AF XY: 0.257 AC XY: 19132 AN XY: 74396

Gnomad4 AFR AF: 0.413

Gnomad4 AMR AF: 0.210

Gnomad4 ASJ AF: 0.223

Gnomad4 EAS AF: 0.119

Gnomad4 SAS AF: 0.149

Gnomad4 FIN AF: 0.141

Gnomad4 NFE AF: 0.229

Gnomad4 OTH AF: 0.238

Alfa AF: 0.242 Hom.: 2529

Bravo AF: 0.275

Asia WGS AF: 0.139 AC: 487 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	7.2
DANN	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17374749; hg19: chr3-136768010;