rs230884

Variant names:

• chr17-15368756-G-T
• rs230884

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;