ENST00000734108.1:n.272+166T>C

Variant names:

• chr8-6922722-T-C
• rs13275170
• ENST00000734108.1:n.272+166T>C

Variant summary

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

The ENST00000734108.1(ENSG00000295932):​n.272+166T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.412 in 152,010 control chromosomes in the GnomAD database, including 13,628 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 0.41 (13628 hom., cov: 32)
• Consequence: ENSG00000295932 ENST00000734108.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.239
• Publications: 3 publications found

Genes affected

ENSG00000295932 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.487 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000295932	ENST00000734108.1	n.272+166T>C		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.413 AC: 62693 AN: 151892 Hom.: 13635 Cov.: 32

Gnomad AFR AF: 0.295

Gnomad AMI AF: 0.492

Gnomad AMR AF: 0.348

Gnomad ASJ AF: 0.525

Gnomad EAS AF: 0.351

Gnomad SAS AF: 0.504

Gnomad FIN AF: 0.422

Gnomad MID AF: 0.522

Gnomad NFE AF: 0.488

Gnomad OTH AF: 0.433

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

GnomAD4 genome AF: 0.412 AC: 62693 AN: 152010 Hom.: 13628 Cov.: 32 AF XY: 0.406 AC XY: 30148 AN XY: 74294

African (AFR) AF: 0.295 AC: 12215 AN: 41450

American (AMR) AF: 0.347 AC: 5301 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.525 AC: 1822 AN: 3472

East Asian (EAS) AF: 0.351 AC: 1811 AN: 5162

South Asian (SAS) AF: 0.503 AC: 2425 AN: 4818

European-Finnish (FIN) AF: 0.422 AC: 4449 AN: 10548

Middle Eastern (MID) AF: 0.517 AC: 152 AN: 294

European-Non Finnish (NFE) AF: 0.488 AC: 33152 AN: 67966

Other (OTH) AF: 0.435 AC: 917 AN: 2110

Alfa AF: 0.463 Hom.: 62498

Bravo AF: 0.399

Asia WGS AF: 0.430 AC: 1499 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	4.3
DANN	Benign	0.60
PhyloP100		0.24

Splicing

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

Other links and lift over

dbSNP: rs13275170; hg19: chr8-6780244;