rs16940565

Variant names:

• chr15-87559804-A-C
• rs16940565
• ENST00000560439.1:n.81-16807T>G

Variant summary

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

The ENST00000560439.1(ENSG00000259560):​n.81-16807T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.106 in 152,192 control chromosomes in the GnomAD database, including 937 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 0.11 (937 hom., cov: 32)
• Consequence: ENSG00000259560 ENST00000560439.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.05
• Publications: 2 publications found

Genes affected

ENSG00000259560 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.125 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000560439.1. 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
	LOC102724465	NR_187944.1		n.84-57998T>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000259560	ENST00000560439.1	TSL:3	n.81-16807T>G		intron	N/A
	ENSG00000259560	ENST00000656130.2		n.203+55967T>G		intron	N/A
	ENSG00000259560	ENST00000665121.1		n.54-57998T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.105 AC: 16041 AN: 152074 Hom.: 934 Cov.: 32

Gnomad AFR AF: 0.0816

Gnomad AMI AF: 0.0923

Gnomad AMR AF: 0.101

Gnomad ASJ AF: 0.164

Gnomad EAS AF: 0.00116

Gnomad SAS AF: 0.127

Gnomad FIN AF: 0.0850

Gnomad MID AF: 0.158

Gnomad NFE AF: 0.127

Gnomad OTH AF: 0.112

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

GnomAD4 genome AF: 0.106 AC: 16060 AN: 152192 Hom.: 937 Cov.: 32 AF XY: 0.104 AC XY: 7726 AN XY: 74406

African (AFR) AF: 0.0819 AC: 3400 AN: 41528

American (AMR) AF: 0.101 AC: 1543 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.164 AC: 568 AN: 3466

East Asian (EAS) AF: 0.000965 AC: 5 AN: 5182

South Asian (SAS) AF: 0.128 AC: 618 AN: 4818

European-Finnish (FIN) AF: 0.0850 AC: 902 AN: 10610

Middle Eastern (MID) AF: 0.153 AC: 45 AN: 294

European-Non Finnish (NFE) AF: 0.127 AC: 8664 AN: 68000

Other (OTH) AF: 0.110 AC: 231 AN: 2108

Alfa AF: 0.125 Hom.: 2021

Bravo AF: 0.103

Asia WGS AF: 0.0650 AC: 229 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	5.0
DANN	Benign	0.59
PhyloP100		1.0

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs16940565;

hg19: chr15-88103035;