rs688220

Positions:

• chr15-34706674-G-A
• chr15-34706674-G-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 0.472 in 151,908 control chromosomes in the GnomAD database, including 17,497 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 0.47 (17497 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.263

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.584 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: 0.472 AC: 71699 AN: 151790 Hom.: 17478 Cov.: 32

Gnomad AFR AF: 0.590

Gnomad AMI AF: 0.654

Gnomad AMR AF: 0.405

Gnomad ASJ AF: 0.385

Gnomad EAS AF: 0.439

Gnomad SAS AF: 0.591

Gnomad FIN AF: 0.348

Gnomad MID AF: 0.332

Gnomad NFE AF: 0.433

Gnomad OTH AF: 0.452

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

GnomAD4 genome AF: 0.472 AC: 71761 AN: 151908 Hom.: 17497 Cov.: 32 AF XY: 0.468 AC XY: 34757 AN XY: 74246

Gnomad4 AFR AF: 0.590

Gnomad4 AMR AF: 0.404

Gnomad4 ASJ AF: 0.385

Gnomad4 EAS AF: 0.439

Gnomad4 SAS AF: 0.590

Gnomad4 FIN AF: 0.348

Gnomad4 NFE AF: 0.433

Gnomad4 OTH AF: 0.453

Alfa AF: 0.351 Hom.: 1423

Bravo AF: 0.478

Asia WGS AF: 0.533 AC: 1853 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	2.8
DANN	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs688220; hg19: chr15-34998875;