rs16949665

Variant names:

• chr15-94905185-G-A
• rs16949665
• ENST00000614581.1:n.237+618G>A

Variant summary

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

The ENST00000614581.1(ENSG00000293024):​n.237+618G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0448 in 152,120 control chromosomes in the GnomAD database, including 430 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 0.045 (430 hom., cov: 32)
• Consequence: ENSG00000293024 ENST00000614581.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.122
• Publications: 1 publications found

Genes affected

ENSG00000293024 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.76).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.138 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000614581.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000293024	ENST00000614581.1	TSL:5	n.237+618G>A		intron	N/A
	ENSG00000293024	ENST00000615751.5	TSL:5	n.130+48322G>A		intron	N/A
	ENSG00000293024	ENST00000618377.1	TSL:5	n.330+48322G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0448 AC: 6809 AN: 152002 Hom.: 431 Cov.: 32

Gnomad AFR AF: 0.141

Gnomad AMI AF: 0.00768

Gnomad AMR AF: 0.0172

Gnomad ASJ AF: 0.00144

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00104

Gnomad FIN AF: 0.00472

Gnomad MID AF: 0.0222

Gnomad NFE AF: 0.00857

Gnomad OTH AF: 0.0292

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

GnomAD4 genome AF: 0.0448 AC: 6816 AN: 152120 Hom.: 430 Cov.: 32 AF XY: 0.0431 AC XY: 3202 AN XY: 74370

African (AFR) AF: 0.141 AC: 5837 AN: 41482

American (AMR) AF: 0.0171 AC: 261 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.00144 AC: 5 AN: 3468

East Asian (EAS) AF: 0.00 AC: 0 AN: 5166

South Asian (SAS) AF: 0.00104 AC: 5 AN: 4810

European-Finnish (FIN) AF: 0.00472 AC: 50 AN: 10596

Middle Eastern (MID) AF: 0.0238 AC: 7 AN: 294

European-Non Finnish (NFE) AF: 0.00857 AC: 583 AN: 68022

Other (OTH) AF: 0.0289 AC: 61 AN: 2110

Alfa AF: 0.0395 Hom.: 58

Bravo AF: 0.0514

Asia WGS AF: 0.00606 AC: 22 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	12
DANN	Benign	0.79
PhyloP100		0.12

Splicing

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

Other links and lift over

dbSNP: rs16949665; hg19: chr15-95448414;