ENST00000783955.1:n.879C>T

Variant names:

• chr6-27758952-C-T
• rs7776351
• ENST00000783955.1:n.879C>T

Variant summary

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

The ENST00000783955.1(ENSG00000287252):​n.879C>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 0.33 in 152,098 control chromosomes in the GnomAD database, including 10,022 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 0.33 (10022 hom., cov: 32)
• Consequence: ENSG00000287252 ENST00000783955.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.949
• Publications: 27 publications found

Genes affected

ENSG00000287252 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.556 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
ENSG00000287252	ENST00000783955.1	n.879C>T		non_coding_transcript_exon_variant	Exon 2 of 2
ENSG00000287252	ENST00000685998.2	n.326+1211C>T		intron_variant	Intron 1 of 4
ENSG00000287252	ENST00000689964.2	n.322+1214C>T		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.330 AC: 50164 AN: 151980 Hom.: 9995 Cov.: 32

Gnomad AFR AF: 0.562

Gnomad AMI AF: 0.389

Gnomad AMR AF: 0.293

Gnomad ASJ AF: 0.162

Gnomad EAS AF: 0.205

Gnomad SAS AF: 0.247

Gnomad FIN AF: 0.190

Gnomad MID AF: 0.212

Gnomad NFE AF: 0.244

Gnomad OTH AF: 0.311

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

GnomAD4 genome AF: 0.330 AC: 50235 AN: 152098 Hom.: 10022 Cov.: 32 AF XY: 0.324 AC XY: 24120 AN XY: 74344

African (AFR) AF: 0.562 AC: 23306 AN: 41470

American (AMR) AF: 0.293 AC: 4479 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.162 AC: 563 AN: 3470

East Asian (EAS) AF: 0.205 AC: 1063 AN: 5176

South Asian (SAS) AF: 0.247 AC: 1189 AN: 4814

European-Finnish (FIN) AF: 0.190 AC: 2013 AN: 10584

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

European-Non Finnish (NFE) AF: 0.243 AC: 16553 AN: 67988

Other (OTH) AF: 0.308 AC: 651 AN: 2112

Alfa AF: 0.272 Hom.: 20540

Bravo AF: 0.349

Asia WGS AF: 0.248 AC: 863 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.8
DANN	Benign	0.67
PhyloP100		-0.95

Splicing

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

Other links and lift over

dbSNP: rs7776351; hg19: chr6-27726731;