rs6662385

Variant names:

• chr1-72707892-C-T
• rs6662385
• ENST00000654386.1:n.437-10087G>A

Variant summary

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

The ENST00000654386.1(ENSG00000225087):​n.437-10087G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.522 in 151,582 control chromosomes in the GnomAD database, including 25,606 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 0.52 (25606 hom., cov: 32)
• Consequence: ENSG00000225087 ENST00000654386.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.276
• Publications: 3 publications found

Genes affected

ENSG00000225087 (HGNC:):

LINC02796 (HGNC:27918): (long intergenic non-protein coding RNA 2796)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.708 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105378798	NR_188684.1	n.282-6829G>A		intron_variant	Intron 3 of 4
LOC105378798	NR_188685.1	n.231-6829G>A		intron_variant	Intron 3 of 4
LOC105378798	NR_188686.1	n.282-10087G>A		intron_variant	Intron 3 of 3
LOC105378798	NR_188687.1	n.203-10087G>A		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000225087	ENST00000654386.1	n.437-10087G>A		intron_variant	Intron 3 of 3
ENSG00000225087	ENST00000660076.1	n.208-10087G>A		intron_variant	Intron 2 of 2
ENSG00000225087	ENST00000661739.1	n.282-10087G>A		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.523 AC: 79190 AN: 151466 Hom.: 25619 Cov.: 32

Gnomad AFR AF: 0.140

Gnomad AMI AF: 0.723

Gnomad AMR AF: 0.646

Gnomad ASJ AF: 0.685

Gnomad EAS AF: 0.231

Gnomad SAS AF: 0.494

Gnomad FIN AF: 0.691

Gnomad MID AF: 0.674

Gnomad NFE AF: 0.714

Gnomad OTH AF: 0.557

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

GnomAD4 genome AF: 0.522 AC: 79172 AN: 151582 Hom.: 25606 Cov.: 32 AF XY: 0.521 AC XY: 38595 AN XY: 74086

African (AFR) AF: 0.140 AC: 5784 AN: 41414

American (AMR) AF: 0.645 AC: 9788 AN: 15170

Ashkenazi Jewish (ASJ) AF: 0.685 AC: 2368 AN: 3458

East Asian (EAS) AF: 0.231 AC: 1178 AN: 5096

South Asian (SAS) AF: 0.495 AC: 2382 AN: 4816

European-Finnish (FIN) AF: 0.691 AC: 7307 AN: 10572

Middle Eastern (MID) AF: 0.663 AC: 195 AN: 294

European-Non Finnish (NFE) AF: 0.714 AC: 48349 AN: 67744

Other (OTH) AF: 0.552 AC: 1162 AN: 2106

Alfa AF: 0.551 Hom.: 5037

Bravo AF: 0.502

Asia WGS AF: 0.353 AC: 1228 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	3.5
DANN	Benign	0.63
PhyloP100		0.28

Splicing

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

Other links and lift over

dbSNP: rs6662385; hg19: chr1-73173575;