ENST00000502766.2:n.436+7393G>T

Variant names:

• chr8-79794718-C-A
• rs2920949
• ENST00000502766.2:n.436+7393G>T

Variant summary

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

The ENST00000502766.2(ENSG00000249328):​n.436+7393G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.388 in 151,630 control chromosomes in the GnomAD database, including 11,550 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 0.39 (11550 hom., cov: 30)
• Consequence: ENSG00000249328 ENST00000502766.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.626
• Publications: 7 publications found

Genes affected

ENSG00000249328 (HGNC:):

LINC01607 (HGNC:51660): (long intergenic non-protein coding RNA 1607)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.452 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC101927040	NR_110954.1	n.436+7393G>T		intron_variant	Intron 4 of 5
LINC01607	NR_125410.1	n.266-7769C>A		intron_variant	Intron 3 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000249328	ENST00000502766.2	n.436+7393G>T		intron_variant	Intron 4 of 5	2
LINC01607	ENST00000607172.1	n.266-7769C>A		intron_variant	Intron 3 of 3	2
LINC01607	ENST00000607754.5	n.160-5843C>A		intron_variant	Intron 1 of 2	3

Frequencies

GnomAD3 genomes AF: 0.388 AC: 58741 AN: 151514 Hom.: 11532 Cov.: 30

Gnomad AFR AF: 0.393

Gnomad AMI AF: 0.340

Gnomad AMR AF: 0.460

Gnomad ASJ AF: 0.398

Gnomad EAS AF: 0.351

Gnomad SAS AF: 0.306

Gnomad FIN AF: 0.360

Gnomad MID AF: 0.351

Gnomad NFE AF: 0.380

Gnomad OTH AF: 0.408

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

GnomAD4 genome AF: 0.388 AC: 58812 AN: 151630 Hom.: 11550 Cov.: 30 AF XY: 0.385 AC XY: 28495 AN XY: 74104

African (AFR) AF: 0.393 AC: 16219 AN: 41258

American (AMR) AF: 0.461 AC: 7034 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.398 AC: 1381 AN: 3468

East Asian (EAS) AF: 0.351 AC: 1810 AN: 5154

South Asian (SAS) AF: 0.307 AC: 1472 AN: 4802

European-Finnish (FIN) AF: 0.360 AC: 3770 AN: 10480

Middle Eastern (MID) AF: 0.367 AC: 108 AN: 294

European-Non Finnish (NFE) AF: 0.380 AC: 25839 AN: 67914

Other (OTH) AF: 0.414 AC: 871 AN: 2106

Alfa AF: 0.385 Hom.: 34663

Bravo AF: 0.402

Asia WGS AF: 0.383 AC: 1334 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	5.6
DANN	Benign	0.52
PhyloP100		0.63

Splicing

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

Other links and lift over

dbSNP: rs2920949; hg19: chr8-80706953;