15-89937354-G-A

Variant names:

• chr15-89937354-G-A
• rs1702161
• ENST00000766695.1:n.46+271C>T

Variant summary

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

The ENST00000766695.1(ENSG00000299833):​n.46+271C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.738 in 151,974 control chromosomes in the GnomAD database, including 45,824 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 0.74 (45824 hom., cov: 31)
• Consequence: ENSG00000299833 ENST00000766695.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.336
• Publications: 2 publications found

Genes affected

ENSG00000299833 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.92 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000766695.1. 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
	ENSG00000299833	ENST00000766695.1		n.46+271C>T		intron	N/A
	ENSG00000299833	ENST00000766696.1		n.267+271C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.739 AC: 112222 AN: 151854 Hom.: 45839 Cov.: 31

Gnomad AFR AF: 0.381

Gnomad AMI AF: 0.912

Gnomad AMR AF: 0.684

Gnomad ASJ AF: 0.948

Gnomad EAS AF: 0.633

Gnomad SAS AF: 0.884

Gnomad FIN AF: 0.896

Gnomad MID AF: 0.905

Gnomad NFE AF: 0.926

Gnomad OTH AF: 0.801

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

GnomAD4 genome AF: 0.738 AC: 112201 AN: 151974 Hom.: 45824 Cov.: 31 AF XY: 0.736 AC XY: 54672 AN XY: 74274

African (AFR) AF: 0.380 AC: 15703 AN: 41362

American (AMR) AF: 0.683 AC: 10405 AN: 15240

Ashkenazi Jewish (ASJ) AF: 0.948 AC: 3286 AN: 3468

East Asian (EAS) AF: 0.633 AC: 3269 AN: 5164

South Asian (SAS) AF: 0.885 AC: 4268 AN: 4824

European-Finnish (FIN) AF: 0.896 AC: 9473 AN: 10574

Middle Eastern (MID) AF: 0.908 AC: 267 AN: 294

European-Non Finnish (NFE) AF: 0.926 AC: 63019 AN: 68022

Other (OTH) AF: 0.794 AC: 1679 AN: 2114

Alfa AF: 0.870 Hom.: 222687

Bravo AF: 0.705

Asia WGS AF: 0.718 AC: 2496 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.1
DANN	Benign	0.78
PhyloP100		-0.34

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: rs1702161;

hg19: chr15-90480586;