rs685352

Variant names:

• chr15-34716134-A-G
• rs685352

Your query was ambiguous. Multiple possible variants found:

• chr15-34716134-A-G
• chr15-34716134-A-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 0.463 in 152,146 control chromosomes in the GnomAD database, including 16,570 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 0.46 (16570 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.271

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.59 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: 0.463 AC: 70359 AN: 152028 Hom.: 16550 Cov.: 33

Gnomad AFR AF: 0.526

Gnomad AMI AF: 0.662

Gnomad AMR AF: 0.443

Gnomad ASJ AF: 0.392

Gnomad EAS AF: 0.451

Gnomad SAS AF: 0.609

Gnomad FIN AF: 0.333

Gnomad MID AF: 0.421

Gnomad NFE AF: 0.441

Gnomad OTH AF: 0.457

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

GnomAD4 genome AF: 0.463 AC: 70422 AN: 152146 Hom.: 16570 Cov.: 33 AF XY: 0.459 AC XY: 34144 AN XY: 74406

Gnomad4 AFR AF: 0.526

Gnomad4 AMR AF: 0.442

Gnomad4 ASJ AF: 0.392

Gnomad4 EAS AF: 0.451

Gnomad4 SAS AF: 0.609

Gnomad4 FIN AF: 0.333

Gnomad4 NFE AF: 0.441

Gnomad4 OTH AF: 0.456

Alfa AF: 0.366 Hom.: 1410

Bravo AF: 0.469

Asia WGS AF: 0.525 AC: 1825 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.72
DANN	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs685352; hg19: chr15-35008335;