ENST00000816098.1:n.292-25718G>A

Variant names:

• chr9-2203938-C-T
• rs6475600
• ENST00000816098.1:n.292-25718G>A

Variant summary

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

The ENST00000816098.1(ENSG00000306181):​n.292-25718G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.309 in 151,878 control chromosomes in the GnomAD database, including 7,410 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 0.31 (7410 hom., cov: 32)
• Consequence: ENSG00000306181 ENST00000816098.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.106
• Publications: 4 publications found

Genes affected

ENSG00000306181 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.403 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000816098.1. 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
	ENSG00000306181	ENST00000816098.1		n.292-25718G>A		intron	N/A
	ENSG00000306181	ENST00000816099.1		n.296-22916G>A		intron	N/A
	ENSG00000306181	ENST00000816100.1		n.273-25718G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.309 AC: 46959 AN: 151760 Hom.: 7396 Cov.: 32

Gnomad AFR AF: 0.340

Gnomad AMI AF: 0.160

Gnomad AMR AF: 0.326

Gnomad ASJ AF: 0.374

Gnomad EAS AF: 0.169

Gnomad SAS AF: 0.419

Gnomad FIN AF: 0.262

Gnomad MID AF: 0.421

Gnomad NFE AF: 0.295

Gnomad OTH AF: 0.323

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

GnomAD4 genome AF: 0.309 AC: 47002 AN: 151878 Hom.: 7410 Cov.: 32 AF XY: 0.310 AC XY: 22985 AN XY: 74208

African (AFR) AF: 0.341 AC: 14103 AN: 41400

American (AMR) AF: 0.326 AC: 4970 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.374 AC: 1297 AN: 3472

East Asian (EAS) AF: 0.168 AC: 868 AN: 5160

South Asian (SAS) AF: 0.419 AC: 2016 AN: 4816

European-Finnish (FIN) AF: 0.262 AC: 2750 AN: 10504

Middle Eastern (MID) AF: 0.439 AC: 129 AN: 294

European-Non Finnish (NFE) AF: 0.295 AC: 20045 AN: 67956

Other (OTH) AF: 0.322 AC: 678 AN: 2104

Alfa AF: 0.310 Hom.: 9525

Bravo AF: 0.314

Asia WGS AF: 0.310 AC: 1083 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.3
DANN	Benign	0.72
PhyloP100		-0.11

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: rs6475600;

hg19: chr9-2203938;

COSMIC: COSV69634459;