rs230884

Positions:

• chr17-15368756-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 0.286 in 151,886 control chromosomes in the GnomAD database, including 6,991 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 (6991 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0240

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.419 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: 0.286 AC: 43398 AN: 151768 Hom.: 6988 Cov.: 32

Gnomad AFR AF: 0.151

Gnomad AMI AF: 0.469

Gnomad AMR AF: 0.427

Gnomad ASJ AF: 0.366

Gnomad EAS AF: 0.277

Gnomad SAS AF: 0.299

Gnomad FIN AF: 0.304

Gnomad MID AF: 0.301

Gnomad NFE AF: 0.326

Gnomad OTH AF: 0.299

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

GnomAD4 genome AF: 0.286 AC: 43395 AN: 151886 Hom.: 6991 Cov.: 32 AF XY: 0.288 AC XY: 21343 AN XY: 74212

Gnomad4 AFR AF: 0.151

Gnomad4 AMR AF: 0.428

Gnomad4 ASJ AF: 0.366

Gnomad4 EAS AF: 0.276

Gnomad4 SAS AF: 0.299

Gnomad4 FIN AF: 0.304

Gnomad4 NFE AF: 0.326

Gnomad4 OTH AF: 0.296

Alfa AF: 0.321 Hom.: 16228

Bravo AF: 0.290

Asia WGS AF: 0.311 AC: 1083 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.95
DANN	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs230884; hg19: chr17-15272073; COSMIC: COSV60076367;