rs16940565

Positions:

• chr15-87559804-A-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000665121.1(ENSG00000259560):​n.54-57998T>G variant causes a intron, non coding transcript 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: ENST00000665121.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.05

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000665121.1	n.54-57998T>G		intron_variant, non_coding_transcript_variant
	ENST00000560439.1	n.81-16807T>G		intron_variant, non_coding_transcript_variant		3

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

Gnomad4 AFR AF: 0.0819

Gnomad4 AMR AF: 0.101

Gnomad4 ASJ AF: 0.164

Gnomad4 EAS AF: 0.000965

Gnomad4 SAS AF: 0.128

Gnomad4 FIN AF: 0.0850

Gnomad4 NFE AF: 0.127

Gnomad4 OTH AF: 0.110

Alfa AF: 0.127 Hom.: 1623

Bravo AF: 0.103

Asia WGS AF: 0.0650 AC: 229 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs16940565; hg19: chr15-88103035;