15-87668715-T-C

Position:

• chr15-87668715-T-C

Variant summary

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

The ENST00000665121.1(ENSG00000259560):​n.53+35058A>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 0.695 in 152,146 control chromosomes in the GnomAD database, including 37,155 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 0.70 (37155 hom., cov: 33)
• Consequence: ENST00000665121.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.764

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.768 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.53+35058A>G		intron_variant, non_coding_transcript_variant
	ENST00000560439.1	n.80+35058A>G		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.696 AC: 105742 AN: 152028 Hom.: 37133 Cov.: 33

Gnomad AFR AF: 0.775

Gnomad AMI AF: 0.568

Gnomad AMR AF: 0.578

Gnomad ASJ AF: 0.596

Gnomad EAS AF: 0.697

Gnomad SAS AF: 0.617

Gnomad FIN AF: 0.729

Gnomad MID AF: 0.557

Gnomad NFE AF: 0.682

Gnomad OTH AF: 0.670

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

GnomAD4 genome AF: 0.695 AC: 105805 AN: 152146 Hom.: 37155 Cov.: 33 AF XY: 0.692 AC XY: 51479 AN XY: 74372

Gnomad4 AFR AF: 0.775

Gnomad4 AMR AF: 0.577

Gnomad4 ASJ AF: 0.596

Gnomad4 EAS AF: 0.697

Gnomad4 SAS AF: 0.616

Gnomad4 FIN AF: 0.729

Gnomad4 NFE AF: 0.682

Gnomad4 OTH AF: 0.667

Alfa AF: 0.439 Hom.: 504

Bravo AF: 0.687

Asia WGS AF: 0.648 AC: 2253 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	2.0
DANN	Benign	0.20

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10468137; hg19: chr15-88211946;