9-114819660-T-C

Variant names:

• chr9-114819660-T-C
• rs2145929
• ENST00000776746.1:n.177-424A>G

Variant summary

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

The ENST00000776746.1(ENSG00000301160):​n.177-424A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.216 in 152,094 control chromosomes in the GnomAD database, including 4,197 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 0.22 (4197 hom., cov: 32)
• Consequence: ENSG00000301160 ENST00000776746.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.48
• Publications: 6 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 = 0.348 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000776746.1. 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
	ENSG00000301160	ENST00000776746.1		n.177-424A>G		intron	N/A
	ENSG00000301160	ENST00000776747.1		n.119-424A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.215 AC: 32734 AN: 151976 Hom.: 4184 Cov.: 32

Gnomad AFR AF: 0.353

Gnomad AMI AF: 0.209

Gnomad AMR AF: 0.219

Gnomad ASJ AF: 0.141

Gnomad EAS AF: 0.195

Gnomad SAS AF: 0.236

Gnomad FIN AF: 0.101

Gnomad MID AF: 0.168

Gnomad NFE AF: 0.154

Gnomad OTH AF: 0.198

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

GnomAD4 genome AF: 0.216 AC: 32786 AN: 152094 Hom.: 4197 Cov.: 32 AF XY: 0.214 AC XY: 15893 AN XY: 74356

African (AFR) AF: 0.353 AC: 14623 AN: 41450

American (AMR) AF: 0.219 AC: 3349 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.141 AC: 488 AN: 3472

East Asian (EAS) AF: 0.196 AC: 1012 AN: 5176

South Asian (SAS) AF: 0.236 AC: 1140 AN: 4824

European-Finnish (FIN) AF: 0.101 AC: 1072 AN: 10602

Middle Eastern (MID) AF: 0.170 AC: 50 AN: 294

European-Non Finnish (NFE) AF: 0.154 AC: 10445 AN: 67988

Other (OTH) AF: 0.198 AC: 417 AN: 2108

Alfa AF: 0.146 Hom.: 1075

Bravo AF: 0.227

Asia WGS AF: 0.219 AC: 762 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.0060
DANN	Benign	0.40
PhyloP100		-1.5

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: rs2145929;

hg19: chr9-117581940;