9-2194227-C-T

Variant names:

• chr9-2194227-C-T
• rs4741652
• ENST00000816098.1:n.292-16007G>A

Variant summary

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

The ENST00000816098.1(ENSG00000306181):​n.292-16007G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.772 in 152,118 control chromosomes in the GnomAD database, including 45,613 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 (45613 hom., cov: 32)
• Consequence: ENSG00000306181 ENST00000816098.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.814
• 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=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.831 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000306181	ENST00000816098.1		n.292-16007G>A		intron	N/A
	ENSG00000306181	ENST00000816099.1		n.296-13205G>A		intron	N/A
	ENSG00000306181	ENST00000816100.1		n.273-16007G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.772 AC: 117288 AN: 152000 Hom.: 45558 Cov.: 32

Gnomad AFR AF: 0.838

Gnomad AMI AF: 0.815

Gnomad AMR AF: 0.828

Gnomad ASJ AF: 0.709

Gnomad EAS AF: 0.688

Gnomad SAS AF: 0.731

Gnomad FIN AF: 0.771

Gnomad MID AF: 0.756

Gnomad NFE AF: 0.731

Gnomad OTH AF: 0.772

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

GnomAD4 genome AF: 0.772 AC: 117406 AN: 152118 Hom.: 45613 Cov.: 32 AF XY: 0.774 AC XY: 57579 AN XY: 74358

African (AFR) AF: 0.838 AC: 34787 AN: 41496

American (AMR) AF: 0.828 AC: 12649 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.709 AC: 2460 AN: 3472

East Asian (EAS) AF: 0.688 AC: 3547 AN: 5158

South Asian (SAS) AF: 0.732 AC: 3530 AN: 4822

European-Finnish (FIN) AF: 0.771 AC: 8164 AN: 10586

Middle Eastern (MID) AF: 0.765 AC: 225 AN: 294

European-Non Finnish (NFE) AF: 0.731 AC: 49661 AN: 67980

Other (OTH) AF: 0.776 AC: 1640 AN: 2114

Alfa AF: 0.740 Hom.: 129752

Bravo AF: 0.781

Asia WGS AF: 0.741 AC: 2576 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.47
DANN	Benign	0.24
PhyloP100		-0.81

Splicing

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

Other links and lift over

dbSNP: rs4741652; hg19: chr9-2194227; COSMIC: COSV56648857;