rs7864653

Variant names:

• chr9-101018841-G-A
• rs7864653
• ENST00000727919.1:n.92+20791C>T

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000727919.1(ENSG00000295090):​n.92+20791C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0577 in 152,306 control chromosomes in the GnomAD database, including 626 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 0.058 (626 hom., cov: 32)
• Consequence: ENSG00000295090 ENST00000727919.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.21
• Publications: 2 publications found

Genes affected

ENSG00000295090 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.32).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.162 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000727919.1. 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
	ENSG00000295090	ENST00000727919.1		n.92+20791C>T		intron	N/A
	ENSG00000295090	ENST00000727920.1		n.91+20791C>T		intron	N/A
	ENSG00000295090	ENST00000727921.1		n.92+20791C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0574 AC: 8743 AN: 152186 Hom.: 614 Cov.: 32

Gnomad AFR AF: 0.164

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.0450

Gnomad ASJ AF: 0.0187

Gnomad EAS AF: 0.0783

Gnomad SAS AF: 0.0186

Gnomad FIN AF: 0.00132

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.00851

Gnomad OTH AF: 0.0431

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

GnomAD4 genome AF: 0.0577 AC: 8791 AN: 152306 Hom.: 626 Cov.: 32 AF XY: 0.0564 AC XY: 4202 AN XY: 74484

African (AFR) AF: 0.165 AC: 6857 AN: 41558

American (AMR) AF: 0.0449 AC: 687 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.0187 AC: 65 AN: 3472

East Asian (EAS) AF: 0.0779 AC: 403 AN: 5174

South Asian (SAS) AF: 0.0180 AC: 87 AN: 4826

European-Finnish (FIN) AF: 0.00132 AC: 14 AN: 10630

Middle Eastern (MID) AF: 0.0272 AC: 8 AN: 294

European-Non Finnish (NFE) AF: 0.00851 AC: 579 AN: 68032

Other (OTH) AF: 0.0426 AC: 90 AN: 2114

Alfa AF: 0.0298 Hom.: 699

Bravo AF: 0.0676

Asia WGS AF: 0.0610 AC: 214 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.32
CADD	Benign	20
DANN	Benign	0.77
PhyloP100		1.2

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: rs7864653;

hg19: chr9-103781123;