chr9-2194030-C-T

Variant names:

• chr9-2194030-C-T
• rs4741651
• ENST00000816098.1:n.292-15810G>A

Variant summary

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

The ENST00000816098.1(ENSG00000306181):​n.292-15810G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.235 in 152,104 control chromosomes in the GnomAD database, including 5,265 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 0.23 (5265 hom., cov: 33)
• Consequence: ENSG00000306181 ENST00000816098.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.15
• Publications: 7 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=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.418 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107987043	XR_001746600.2	n.298-13008G>A		intron_variant	Intron 2 of 3
LOC107987043	XR_007061395.1	n.302-13008G>A		intron_variant	Intron 2 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000306181	ENST00000816098.1	n.292-15810G>A		intron_variant	Intron 2 of 4
ENSG00000306181	ENST00000816099.1	n.296-13008G>A		intron_variant	Intron 2 of 3
ENSG00000306181	ENST00000816100.1	n.273-15810G>A		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.234 AC: 35630 AN: 151986 Hom.: 5245 Cov.: 33

Gnomad AFR AF: 0.423

Gnomad AMI AF: 0.0877

Gnomad AMR AF: 0.212

Gnomad ASJ AF: 0.143

Gnomad EAS AF: 0.226

Gnomad SAS AF: 0.261

Gnomad FIN AF: 0.138

Gnomad MID AF: 0.174

Gnomad NFE AF: 0.146

Gnomad OTH AF: 0.229

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

GnomAD4 genome AF: 0.235 AC: 35693 AN: 152104 Hom.: 5265 Cov.: 33 AF XY: 0.234 AC XY: 17428 AN XY: 74358

African (AFR) AF: 0.423 AC: 17541 AN: 41454

American (AMR) AF: 0.212 AC: 3250 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.143 AC: 496 AN: 3466

East Asian (EAS) AF: 0.225 AC: 1166 AN: 5176

South Asian (SAS) AF: 0.262 AC: 1262 AN: 4824

European-Finnish (FIN) AF: 0.138 AC: 1463 AN: 10588

Middle Eastern (MID) AF: 0.184 AC: 54 AN: 294

European-Non Finnish (NFE) AF: 0.146 AC: 9904 AN: 67984

Other (OTH) AF: 0.226 AC: 477 AN: 2110

Alfa AF: 0.186 Hom.: 1558

Bravo AF: 0.250

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.33
DANN	Benign	0.49
PhyloP100		-2.2

Splicing

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

Other links and lift over

dbSNP: rs4741651; hg19: chr9-2194030; COSMIC: COSV56648853;