rs16960326

Variant names:

• chr15-47905294-A-G
• rs16960326
• ENST00000560900.1:n.195+20790A>G

Your query was ambiguous. Multiple possible variants found:

• chr15-47905294-A-G
• chr15-47905294-A-T

Variant summary

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

The ENST00000560900.1(ENSG00000259754):​n.195+20790A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.019 in 152,122 control chromosomes in the GnomAD database, including 95 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 0.019 (95 hom., cov: 31)
• Consequence: ENSG00000259754 ENST00000560900.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.111
• Publications: 1 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=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.128 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000560900.1. 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	ENST00000560900.1	TSL:4	n.195+20790A>G		intron	N/A
	ENSG00000259754	ENST00000662551.1		n.189-87415A>G		intron	N/A
	ENSG00000259754	ENST00000664705.1		n.189-87415A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0189 AC: 2876 AN: 152004 Hom.: 94 Cov.: 31

Gnomad AFR AF: 0.0178

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0335

Gnomad ASJ AF: 0.00605

Gnomad EAS AF: 0.137

Gnomad SAS AF: 0.0671

Gnomad FIN AF: 0.00340

Gnomad MID AF: 0.00316

Gnomad NFE AF: 0.00729

Gnomad OTH AF: 0.0197

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

GnomAD4 genome AF: 0.0190 AC: 2883 AN: 152122 Hom.: 95 Cov.: 31 AF XY: 0.0200 AC XY: 1489 AN XY: 74372

African (AFR) AF: 0.0178 AC: 738 AN: 41506

American (AMR) AF: 0.0337 AC: 515 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.00605 AC: 21 AN: 3472

East Asian (EAS) AF: 0.136 AC: 703 AN: 5164

South Asian (SAS) AF: 0.0668 AC: 321 AN: 4808

European-Finnish (FIN) AF: 0.00340 AC: 36 AN: 10594

Middle Eastern (MID) AF: 0.00340 AC: 1 AN: 294

European-Non Finnish (NFE) AF: 0.00729 AC: 496 AN: 67996

Other (OTH) AF: 0.0247 AC: 52 AN: 2108

Alfa AF: 0.0112 Hom.: 30

Bravo AF: 0.0225

Asia WGS AF: 0.116 AC: 403 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	2.9
DANN	Benign	0.70
PhyloP100		0.11

Splicing

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

Other links and lift over

dbSNP: rs16960326; hg19: chr15-48197491;