rs4741651

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.

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.292-15810G>A		intron	N/A
	ENSG00000306181	ENST00000816099.1		n.296-13008G>A		intron	N/A
	ENSG00000306181	ENST00000816100.1		n.273-15810G>A		intron	N/A

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 v4.9

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs4741651;

hg19: chr9-2194030;

COSMIC: COSV56648853;