15-94714049-T-C

Variant names:

• chr15-94714049-T-C
• rs2388779
• ENST00000801102.1:n.159-145A>G

Variant summary

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

The ENST00000801102.1(ENSG00000286917):​n.159-145A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.735 in 152,156 control chromosomes in the GnomAD database, including 41,473 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 0.73 (41473 hom., cov: 33)
• Consequence: ENSG00000286917 ENST00000801102.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.460
• Publications: 3 publications found

Genes affected

ENSG00000286917 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.797 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000801102.1. 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
	ENSG00000286917	ENST00000801102.1		n.159-145A>G		intron	N/A
	ENSG00000286917	ENST00000801103.1		n.57-145A>G		intron	N/A
	ENSG00000286917	ENST00000801104.1		n.134-145A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.735 AC: 111720 AN: 152038 Hom.: 41422 Cov.: 33

Gnomad AFR AF: 0.804

Gnomad AMI AF: 0.626

Gnomad AMR AF: 0.786

Gnomad ASJ AF: 0.787

Gnomad EAS AF: 0.801

Gnomad SAS AF: 0.807

Gnomad FIN AF: 0.685

Gnomad MID AF: 0.804

Gnomad NFE AF: 0.678

Gnomad OTH AF: 0.734

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

GnomAD4 genome AF: 0.735 AC: 111826 AN: 152156 Hom.: 41473 Cov.: 33 AF XY: 0.740 AC XY: 55003 AN XY: 74352

African (AFR) AF: 0.804 AC: 33368 AN: 41510

American (AMR) AF: 0.785 AC: 12008 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.787 AC: 2732 AN: 3472

East Asian (EAS) AF: 0.802 AC: 4146 AN: 5170

South Asian (SAS) AF: 0.807 AC: 3889 AN: 4818

European-Finnish (FIN) AF: 0.685 AC: 7247 AN: 10586

Middle Eastern (MID) AF: 0.806 AC: 237 AN: 294

European-Non Finnish (NFE) AF: 0.678 AC: 46084 AN: 67990

Other (OTH) AF: 0.730 AC: 1544 AN: 2116

Alfa AF: 0.706 Hom.: 48085

Bravo AF: 0.747

Asia WGS AF: 0.785 AC: 2727 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.1
DANN	Benign	0.44
PhyloP100		-0.46

Splicing

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

Other links and lift over

dbSNP: rs2388779; hg19: chr15-95257278;