ENST00000762879.1:n.272C>T

Variant names:

• chr6-90587361-C-T
• rs282071
• ENST00000762879.1:n.272C>T

Variant summary

Our verdict is Benign. The variant received -9 ACMG points: 0P and 9B. BP4 BA1

The ENST00000762879.1(ENSG00000299366):​n.272C>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 0.631 in 151,974 control chromosomes in the GnomAD database, including 30,564 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 0.63 (30564 hom., cov: 32)
• Consequence: ENSG00000299366 ENST00000762879.1 non_coding_transcript_exon
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -1.38
• Publications: 5 publications found

Genes affected

ENSG00000299366 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -9 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.18).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.672 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124901363	XR_007059679.1	n.149C>T		non_coding_transcript_exon_variant	Exon 1 of 3
LOC124901363	XR_007059680.1	n.568C>T		non_coding_transcript_exon_variant	Exon 1 of 2
LOC124901363	XR_007059681.1	n.171C>T		non_coding_transcript_exon_variant	Exon 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000299366	ENST00000762879.1	n.272C>T		non_coding_transcript_exon_variant	Exon 1 of 4
ENSG00000299366	ENST00000762880.1	n.237C>T		non_coding_transcript_exon_variant	Exon 1 of 4
ENSG00000299366	ENST00000762881.1	n.175C>T		non_coding_transcript_exon_variant	Exon 1 of 3

Frequencies

GnomAD3 genomes AF: 0.631 AC: 95788 AN: 151856 Hom.: 30550 Cov.: 32

Gnomad AFR AF: 0.579

Gnomad AMI AF: 0.584

Gnomad AMR AF: 0.587

Gnomad ASJ AF: 0.783

Gnomad EAS AF: 0.433

Gnomad SAS AF: 0.648

Gnomad FIN AF: 0.631

Gnomad MID AF: 0.742

Gnomad NFE AF: 0.677

Gnomad OTH AF: 0.669

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

GnomAD4 genome AF: 0.631 AC: 95835 AN: 151974 Hom.: 30564 Cov.: 32 AF XY: 0.626 AC XY: 46489 AN XY: 74270

African (AFR) AF: 0.578 AC: 23947 AN: 41432

American (AMR) AF: 0.587 AC: 8967 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.783 AC: 2717 AN: 3468

East Asian (EAS) AF: 0.433 AC: 2231 AN: 5150

South Asian (SAS) AF: 0.648 AC: 3119 AN: 4810

European-Finnish (FIN) AF: 0.631 AC: 6660 AN: 10558

Middle Eastern (MID) AF: 0.729 AC: 213 AN: 292

European-Non Finnish (NFE) AF: 0.677 AC: 46028 AN: 67966

Other (OTH) AF: 0.674 AC: 1420 AN: 2108

Alfa AF: 0.653 Hom.: 8033

Bravo AF: 0.621

Asia WGS AF: 0.570 AC: 1984 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Nov 12, 2018

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.18
CADD	Benign	7.5
DANN	Benign	0.94
PhyloP100		-1.4
PromoterAI		-0.011	Neutral

Splicing

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

Other links and lift over

dbSNP: rs282071; hg19: chr6-91297080; COSMIC: COSV65235343;