ENST00000667253.2:n.65-2780T>C

Variant names:

• chr9-97407570-A-G
• rs1462091
• ENST00000667253.2:n.65-2780T>C

Variant summary

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

The ENST00000667253.2(ENSG00000286375):​n.65-2780T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.31 in 151,824 control chromosomes in the GnomAD database, including 7,317 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 0.31 (7317 hom., cov: 31)
• Consequence: ENSG00000286375 ENST00000667253.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.788
• Publications: 3 publications found

Genes affected

ENSG00000286375 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.333 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
ENSG00000286375	ENST00000667253.2	n.65-2780T>C		intron_variant	Intron 1 of 1
ENSG00000286375	ENST00000778879.1	n.57+4288T>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.310 AC: 47012 AN: 151706 Hom.: 7314 Cov.: 31

Gnomad AFR AF: 0.338

Gnomad AMI AF: 0.333

Gnomad AMR AF: 0.274

Gnomad ASJ AF: 0.406

Gnomad EAS AF: 0.273

Gnomad SAS AF: 0.252

Gnomad FIN AF: 0.273

Gnomad MID AF: 0.339

Gnomad NFE AF: 0.308

Gnomad OTH AF: 0.318

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

GnomAD4 genome AF: 0.310 AC: 47034 AN: 151824 Hom.: 7317 Cov.: 31 AF XY: 0.308 AC XY: 22866 AN XY: 74206

African (AFR) AF: 0.338 AC: 13978 AN: 41348

American (AMR) AF: 0.274 AC: 4178 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.406 AC: 1408 AN: 3468

East Asian (EAS) AF: 0.272 AC: 1408 AN: 5172

South Asian (SAS) AF: 0.253 AC: 1214 AN: 4806

European-Finnish (FIN) AF: 0.273 AC: 2874 AN: 10536

Middle Eastern (MID) AF: 0.330 AC: 97 AN: 294

European-Non Finnish (NFE) AF: 0.308 AC: 20907 AN: 67922

Other (OTH) AF: 0.317 AC: 666 AN: 2104

Alfa AF: 0.312 Hom.: 20864

Bravo AF: 0.312

Asia WGS AF: 0.268 AC: 937 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.54
DANN	Benign	0.56
PhyloP100		-0.79

Splicing

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

Other links and lift over

dbSNP: rs1462091; hg19: chr9-100169852;