9-74091446-C-T

Variant names:

• chr9-74091446-C-T
• rs10781185
• ENST00000793186.1:n.246+5266C>T

Variant summary

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

The ENST00000793186.1(ENSG00000303250):​n.246+5266C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.289 in 151,940 control chromosomes in the GnomAD database, including 6,706 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 0.29 (6706 hom., cov: 31)
• Consequence: ENSG00000303250 ENST00000793186.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.857
• Publications: 1 publications found

Genes affected

ENSG00000303250 (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 (EAS) allele frequency at 95% confidence interval = 0.541 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000793186.1. 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
	ENSG00000303250	ENST00000793186.1		n.246+5266C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.289 AC: 43935 AN: 151822 Hom.: 6715 Cov.: 31

Gnomad AFR AF: 0.255

Gnomad AMI AF: 0.338

Gnomad AMR AF: 0.353

Gnomad ASJ AF: 0.243

Gnomad EAS AF: 0.559

Gnomad SAS AF: 0.326

Gnomad FIN AF: 0.242

Gnomad MID AF: 0.220

Gnomad NFE AF: 0.282

Gnomad OTH AF: 0.309

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

GnomAD4 genome AF: 0.289 AC: 43940 AN: 151940 Hom.: 6706 Cov.: 31 AF XY: 0.290 AC XY: 21547 AN XY: 74250

African (AFR) AF: 0.255 AC: 10553 AN: 41432

American (AMR) AF: 0.353 AC: 5390 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.243 AC: 842 AN: 3468

East Asian (EAS) AF: 0.558 AC: 2866 AN: 5138

South Asian (SAS) AF: 0.325 AC: 1565 AN: 4816

European-Finnish (FIN) AF: 0.242 AC: 2550 AN: 10558

Middle Eastern (MID) AF: 0.233 AC: 68 AN: 292

European-Non Finnish (NFE) AF: 0.282 AC: 19156 AN: 67956

Other (OTH) AF: 0.304 AC: 642 AN: 2112

Alfa AF: 0.289 Hom.: 2767

Bravo AF: 0.303

Asia WGS AF: 0.403 AC: 1403 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	3.5
DANN	Benign	0.77
PhyloP100		-0.86

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: rs10781185;

hg19: chr9-76706362;