chr9-114814199-C-T

Variant names:

• chr9-114814199-C-T
• rs7865494
• ENST00000776746.1:n.454-2197G>A

Variant summary

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

The ENST00000776746.1(ENSG00000301160):​n.454-2197G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.195 in 151,856 control chromosomes in the GnomAD database, including 3,249 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 0.19 (3249 hom., cov: 32)
• Consequence: ENSG00000301160 ENST00000776746.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.52
• Publications: 13 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=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.283 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	ENST00000776746.1	n.454-2197G>A		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.195 AC: 29541 AN: 151738 Hom.: 3245 Cov.: 32

Gnomad AFR AF: 0.288

Gnomad AMI AF: 0.209

Gnomad AMR AF: 0.210

Gnomad ASJ AF: 0.137

Gnomad EAS AF: 0.194

Gnomad SAS AF: 0.232

Gnomad FIN AF: 0.101

Gnomad MID AF: 0.165

Gnomad NFE AF: 0.150

Gnomad OTH AF: 0.185

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

GnomAD4 genome AF: 0.195 AC: 29580 AN: 151856 Hom.: 3249 Cov.: 32 AF XY: 0.194 AC XY: 14427 AN XY: 74192

African (AFR) AF: 0.288 AC: 11898 AN: 41370

American (AMR) AF: 0.210 AC: 3211 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.137 AC: 476 AN: 3464

East Asian (EAS) AF: 0.195 AC: 1002 AN: 5148

South Asian (SAS) AF: 0.232 AC: 1114 AN: 4794

European-Finnish (FIN) AF: 0.101 AC: 1068 AN: 10532

Middle Eastern (MID) AF: 0.167 AC: 49 AN: 294

European-Non Finnish (NFE) AF: 0.150 AC: 10184 AN: 67962

Other (OTH) AF: 0.184 AC: 388 AN: 2108

Alfa AF: 0.183 Hom.: 652

Bravo AF: 0.203

Asia WGS AF: 0.210 AC: 730 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.22
DANN	Benign	0.54
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs7865494; hg19: chr9-117576479;