9-136374886-C-T

Variant names:

• chr9-136374886-C-T
• rs10781500
• ENST00000772719.1:n.1351C>T

Variant summary

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

The ENST00000772719.1(ENSG00000300558):​n.1351C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.378 in 152,098 control chromosomes in the GnomAD database, including 11,281 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 0.38 (11281 hom., cov: 34)
• Consequence: ENSG00000300558 ENST00000772719.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.01
• Publications: 66 publications found

Genes affected

ENSG00000300558 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.463 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000772719.1. 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
	ENSG00000300558	ENST00000772719.1		n.1351C>T		non_coding_transcript_exon	Exon 3 of 3

Frequencies

GnomAD3 genomes AF: 0.378 AC: 57446 AN: 151980 Hom.: 11263 Cov.: 34

Gnomad AFR AF: 0.286

Gnomad AMI AF: 0.414

Gnomad AMR AF: 0.472

Gnomad ASJ AF: 0.355

Gnomad EAS AF: 0.310

Gnomad SAS AF: 0.330

Gnomad FIN AF: 0.412

Gnomad MID AF: 0.199

Gnomad NFE AF: 0.418

Gnomad OTH AF: 0.352

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

GnomAD4 genome AF: 0.378 AC: 57513 AN: 152098 Hom.: 11281 Cov.: 34 AF XY: 0.377 AC XY: 28000 AN XY: 74350

African (AFR) AF: 0.287 AC: 11889 AN: 41470

American (AMR) AF: 0.472 AC: 7226 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.355 AC: 1233 AN: 3470

East Asian (EAS) AF: 0.309 AC: 1601 AN: 5174

South Asian (SAS) AF: 0.330 AC: 1593 AN: 4832

European-Finnish (FIN) AF: 0.412 AC: 4358 AN: 10574

Middle Eastern (MID) AF: 0.214 AC: 63 AN: 294

European-Non Finnish (NFE) AF: 0.418 AC: 28424 AN: 67968

Other (OTH) AF: 0.355 AC: 748 AN: 2110

Alfa AF: 0.394 Hom.: 33908

Bravo AF: 0.376

Asia WGS AF: 0.385 AC: 1339 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	7.1
DANN	Benign	0.55
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs10781500; hg19: chr9-139269338; COSMIC: COSV53731742;