rs10493928

Variant names:

• chr1-100561702-A-G
• rs10493928
• ENST00000773974.1:n.165-2409T>C

Variant summary

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

The ENST00000773974.1(LINC01349):​n.165-2409T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.105 in 152,140 control chromosomes in the GnomAD database, including 1,006 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 0.11 (1006 hom., cov: 32)
• Consequence: LINC01349 ENST00000773974.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.422
• Publications: 0 publications found

Genes affected

LINC01349 (HGNC:50568): (long intergenic non-protein coding RNA 1349)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.165 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
LINC01349	ENST00000773974.1	n.165-2409T>C		intron_variant	Intron 3 of 3
LINC01349	ENST00000773975.1	n.125-2409T>C		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.105 AC: 16006 AN: 152022 Hom.: 1005 Cov.: 32

Gnomad AFR AF: 0.168

Gnomad AMI AF: 0.0800

Gnomad AMR AF: 0.0874

Gnomad ASJ AF: 0.0589

Gnomad EAS AF: 0.0829

Gnomad SAS AF: 0.0877

Gnomad FIN AF: 0.104

Gnomad MID AF: 0.0955

Gnomad NFE AF: 0.0768

Gnomad OTH AF: 0.108

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

GnomAD4 genome AF: 0.105 AC: 16018 AN: 152140 Hom.: 1006 Cov.: 32 AF XY: 0.105 AC XY: 7827 AN XY: 74370

African (AFR) AF: 0.168 AC: 6973 AN: 41528

American (AMR) AF: 0.0876 AC: 1338 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.0589 AC: 204 AN: 3464

East Asian (EAS) AF: 0.0823 AC: 427 AN: 5186

South Asian (SAS) AF: 0.0878 AC: 424 AN: 4828

European-Finnish (FIN) AF: 0.104 AC: 1105 AN: 10606

Middle Eastern (MID) AF: 0.0890 AC: 26 AN: 292

European-Non Finnish (NFE) AF: 0.0768 AC: 5217 AN: 67942

Other (OTH) AF: 0.110 AC: 231 AN: 2106

Alfa AF: 0.0894 Hom.: 128

Bravo AF: 0.106

Asia WGS AF: 0.104 AC: 360 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	10
DANN	Benign	0.78
PhyloP100		-0.42

Splicing

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

Other links and lift over

dbSNP: rs10493928; hg19: chr1-101027258;