rs17466389

Variant names:

• chr15-48815443-G-C
• rs17466389

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.122 in 152,186 control chromosomes in the GnomAD database, including 1,633 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 0.12 (1633 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.72
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.53).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.159 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: 0.122 AC: 18584 AN: 152068 Hom.: 1633 Cov.: 32

Gnomad AFR AF: 0.0308

Gnomad AMI AF: 0.213

Gnomad AMR AF: 0.0830

Gnomad ASJ AF: 0.100

Gnomad EAS AF: 0.0820

Gnomad SAS AF: 0.150

Gnomad FIN AF: 0.302

Gnomad MID AF: 0.0633

Gnomad NFE AF: 0.161

Gnomad OTH AF: 0.0842

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

GnomAD4 genome AF: 0.122 AC: 18591 AN: 152186 Hom.: 1633 Cov.: 32 AF XY: 0.127 AC XY: 9480 AN XY: 74388

African (AFR) AF: 0.0307 AC: 1277 AN: 41536

American (AMR) AF: 0.0834 AC: 1276 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.100 AC: 348 AN: 3468

East Asian (EAS) AF: 0.0820 AC: 425 AN: 5184

South Asian (SAS) AF: 0.151 AC: 725 AN: 4816

European-Finnish (FIN) AF: 0.302 AC: 3193 AN: 10562

Middle Eastern (MID) AF: 0.0680 AC: 20 AN: 294

European-Non Finnish (NFE) AF: 0.161 AC: 10955 AN: 68012

Other (OTH) AF: 0.0843 AC: 178 AN: 2112

Alfa AF: 0.147 Hom.: 234

Bravo AF: 0.101

Asia WGS AF: 0.135 AC: 472 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.53
CADD	Benign	12
DANN	Benign	0.65
PhyloP100		1.7

Splicing

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

Other links and lift over

dbSNP: rs17466389; hg19: chr15-49107640;