rs16960244

Variant names:

• chr15-47862385-T-C
• rs16960244
• ENST00000662551.1:n.188+49469T>C

Variant summary

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

The ENST00000662551.1(ENSG00000259754):​n.188+49469T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.104 in 152,274 control chromosomes in the GnomAD database, including 1,431 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 0.10 (1431 hom., cov: 32)
• Consequence: ENSG00000259754 ENST00000662551.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.144
• Publications: 0 publications found

Genes affected

ENSG00000259754 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.226 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000662551.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000259754	ENST00000662551.1		n.188+49469T>C		intron	N/A
	ENSG00000259754	ENST00000664705.1		n.188+49469T>C		intron	N/A
	ENSG00000259754	ENST00000665188.1		n.68+49469T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.103 AC: 15748 AN: 152156 Hom.: 1426 Cov.: 32

Gnomad AFR AF: 0.229

Gnomad AMI AF: 0.00548

Gnomad AMR AF: 0.0566

Gnomad ASJ AF: 0.0784

Gnomad EAS AF: 0.131

Gnomad SAS AF: 0.229

Gnomad FIN AF: 0.0389

Gnomad MID AF: 0.0510

Gnomad NFE AF: 0.0401

Gnomad OTH AF: 0.0808

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

GnomAD4 genome AF: 0.104 AC: 15783 AN: 152274 Hom.: 1431 Cov.: 32 AF XY: 0.105 AC XY: 7810 AN XY: 74452

African (AFR) AF: 0.229 AC: 9529 AN: 41538

American (AMR) AF: 0.0566 AC: 866 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0784 AC: 272 AN: 3470

East Asian (EAS) AF: 0.130 AC: 677 AN: 5194

South Asian (SAS) AF: 0.229 AC: 1102 AN: 4822

European-Finnish (FIN) AF: 0.0389 AC: 413 AN: 10616

Middle Eastern (MID) AF: 0.0476 AC: 14 AN: 294

European-Non Finnish (NFE) AF: 0.0400 AC: 2723 AN: 68018

Other (OTH) AF: 0.0861 AC: 182 AN: 2114

Alfa AF: 0.0918 Hom.: 193

Bravo AF: 0.107

Asia WGS AF: 0.203 AC: 703 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	13
DANN	Benign	0.81
PhyloP100		-0.14

Splicing

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

Other links and lift over

dbSNP: rs16960244; hg19: chr15-48154582;