rs282071

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -11 ACMG points: 0P and 11B. BP4 BP6_Moderate 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. Variant has been reported in ClinVar as Benign (★).

• 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 -11 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.18).
• BP6: Variant 6-90587361-C-T is Benign according to our data. Variant chr6-90587361-C-T is described in ClinVar as Benign. ClinVar VariationId is 1228113.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.672 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000762879.1. 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
	ENSG00000299366	ENST00000762879.1		n.272C>T		non_coding_transcript_exon	Exon 1 of 4
	ENSG00000299366	ENST00000762880.1		n.237C>T		non_coding_transcript_exon	Exon 1 of 4
	ENSG00000299366	ENST00000762881.1		n.175C>T		non_coding_transcript_exon	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

ClinVar submissions

Significance: Benign

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	-	1	not provided (1)

Computational scores

Source: dbNSFP v4.9

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs282071;

hg19: chr6-91297080;

COSMIC: COSV65235343;