9-2234701-T-C

Variant names:

• chr9-2234701-T-C
• rs10811679
• ENST00000816098.1:n.184-4013A>G

Variant summary

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

The ENST00000816098.1(ENSG00000306181):​n.184-4013A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.559 in 152,074 control chromosomes in the GnomAD database, including 26,051 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 0.56 (26051 hom., cov: 32)
• Consequence: ENSG00000306181 ENST00000816098.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.558
• Publications: 5 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=-0.79).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.674 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.184-4013A>G		intron	N/A
	ENSG00000306181	ENST00000816099.1		n.188-4013A>G		intron	N/A
	ENSG00000306181	ENST00000816100.1		n.165-4013A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.559 AC: 84970 AN: 151954 Hom.: 26047 Cov.: 32

Gnomad AFR AF: 0.281

Gnomad AMI AF: 0.694

Gnomad AMR AF: 0.685

Gnomad ASJ AF: 0.709

Gnomad EAS AF: 0.604

Gnomad SAS AF: 0.621

Gnomad FIN AF: 0.628

Gnomad MID AF: 0.611

Gnomad NFE AF: 0.670

Gnomad OTH AF: 0.628

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

GnomAD4 genome AF: 0.559 AC: 84998 AN: 152074 Hom.: 26051 Cov.: 32 AF XY: 0.562 AC XY: 41793 AN XY: 74334

African (AFR) AF: 0.280 AC: 11632 AN: 41492

American (AMR) AF: 0.685 AC: 10475 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.709 AC: 2459 AN: 3470

East Asian (EAS) AF: 0.605 AC: 3126 AN: 5164

South Asian (SAS) AF: 0.619 AC: 2986 AN: 4822

European-Finnish (FIN) AF: 0.628 AC: 6636 AN: 10572

Middle Eastern (MID) AF: 0.599 AC: 176 AN: 294

European-Non Finnish (NFE) AF: 0.670 AC: 45550 AN: 67958

Other (OTH) AF: 0.630 AC: 1325 AN: 2102

Alfa AF: 0.575 Hom.: 5661

Bravo AF: 0.554

Asia WGS AF: 0.622 AC: 2159 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	8.2
DANN	Benign	0.84
PhyloP100		-0.56

Splicing

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

Other links and lift over

dbSNP: rs10811679; hg19: chr9-2234701; COSMIC: COSV69442541;