9-114818634-C-T

Variant names:

• chr9-114818634-C-T
• rs7869487
• ENST00000776747.1:n.721G>A

Variant summary

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

The ENST00000776747.1(ENSG00000301160):​n.721G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.768 in 151,966 control chromosomes in the GnomAD database, including 45,792 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 0.77 (45792 hom., cov: 30)
• Consequence: ENSG00000301160 ENST00000776747.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.173
• Publications: 24 publications found

Genes affected

ENSG00000301160 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 = 0.916 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000301160	ENST00000776747.1	n.721G>A		non_coding_transcript_exon_variant	Exon 2 of 2
ENSG00000301160	ENST00000776746.1	n.287-249G>A		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.768 AC: 116633 AN: 151846 Hom.: 45717 Cov.: 30

Gnomad AFR AF: 0.923

Gnomad AMI AF: 0.700

Gnomad AMR AF: 0.794

Gnomad ASJ AF: 0.789

Gnomad EAS AF: 0.562

Gnomad SAS AF: 0.757

Gnomad FIN AF: 0.728

Gnomad MID AF: 0.771

Gnomad NFE AF: 0.691

Gnomad OTH AF: 0.744

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

GnomAD4 genome AF: 0.768 AC: 116773 AN: 151966 Hom.: 45792 Cov.: 30 AF XY: 0.770 AC XY: 57204 AN XY: 74288

African (AFR) AF: 0.924 AC: 38317 AN: 41486

American (AMR) AF: 0.795 AC: 12142 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.789 AC: 2739 AN: 3472

East Asian (EAS) AF: 0.562 AC: 2889 AN: 5140

South Asian (SAS) AF: 0.757 AC: 3631 AN: 4796

European-Finnish (FIN) AF: 0.728 AC: 7685 AN: 10562

Middle Eastern (MID) AF: 0.779 AC: 229 AN: 294

European-Non Finnish (NFE) AF: 0.691 AC: 46932 AN: 67926

Other (OTH) AF: 0.746 AC: 1573 AN: 2108

Alfa AF: 0.754 Hom.: 5985

Bravo AF: 0.777

Asia WGS AF: 0.720 AC: 2504 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	1.8
DANN	Benign	0.39
PhyloP100		0.17

Splicing

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

Other links and lift over

dbSNP: rs7869487; hg19: chr9-117580914;