ENST00000754421.1:n.441-16892G>A

Variant names:

• chr10-42998449-C-T
• rs947699
• ENST00000754421.1:n.441-16892G>A

Variant summary

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

The ENST00000754421.1(LINC01264):​n.441-16892G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.148 in 152,190 control chromosomes in the GnomAD database, including 1,991 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 0.15 (1991 hom., cov: 32)
• Consequence: LINC01264 ENST00000754421.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.55
• Publications: 2 publications found

Genes affected

LINC01264 (HGNC:50282): (long intergenic non-protein coding RNA 1264)

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 (EAS) allele frequency at 95% confidence interval = 0.341 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
LINC01264	ENST00000754421.1	n.441-16892G>A		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.148 AC: 22561 AN: 152072 Hom.: 1988 Cov.: 32

Gnomad AFR AF: 0.0871

Gnomad AMI AF: 0.182

Gnomad AMR AF: 0.134

Gnomad ASJ AF: 0.152

Gnomad EAS AF: 0.355

Gnomad SAS AF: 0.199

Gnomad FIN AF: 0.214

Gnomad MID AF: 0.137

Gnomad NFE AF: 0.159

Gnomad OTH AF: 0.144

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

GnomAD4 genome AF: 0.148 AC: 22588 AN: 152190 Hom.: 1991 Cov.: 32 AF XY: 0.154 AC XY: 11445 AN XY: 74396

African (AFR) AF: 0.0872 AC: 3623 AN: 41532

American (AMR) AF: 0.134 AC: 2051 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.152 AC: 527 AN: 3470

East Asian (EAS) AF: 0.354 AC: 1830 AN: 5166

South Asian (SAS) AF: 0.199 AC: 961 AN: 4828

European-Finnish (FIN) AF: 0.214 AC: 2268 AN: 10588

Middle Eastern (MID) AF: 0.140 AC: 41 AN: 292

European-Non Finnish (NFE) AF: 0.159 AC: 10802 AN: 68000

Other (OTH) AF: 0.151 AC: 319 AN: 2116

Alfa AF: 0.152 Hom.: 1062

Bravo AF: 0.140

Asia WGS AF: 0.252 AC: 876 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	2.8
DANN	Benign	0.80
PhyloP100		-1.6

Splicing

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

Other links and lift over

dbSNP: rs947699; hg19: chr10-43493897;