rs271738

Variant names:

• chr1-234527144-G-A
• rs271738
• ENST00000804324.1:n.261+4384C>T

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000804324.1(LINC01354):​n.261+4384C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.529 in 152,068 control chromosomes in the GnomAD database, including 23,292 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 0.53 (23292 hom., cov: 33)
• Consequence: LINC01354 ENST00000804324.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0680
• Publications: 12 publications found

Genes affected

LINC01354 (HGNC:50581): (long intergenic non-protein coding RNA 1354)

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.27).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.917 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
LINC01354	ENST00000804324.1	n.261+4384C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.529 AC: 80333 AN: 151950 Hom.: 23256 Cov.: 33

Gnomad AFR AF: 0.698

Gnomad AMI AF: 0.468

Gnomad AMR AF: 0.589

Gnomad ASJ AF: 0.447

Gnomad EAS AF: 0.939

Gnomad SAS AF: 0.786

Gnomad FIN AF: 0.370

Gnomad MID AF: 0.598

Gnomad NFE AF: 0.392

Gnomad OTH AF: 0.523

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

GnomAD4 genome AF: 0.529 AC: 80429 AN: 152068 Hom.: 23292 Cov.: 33 AF XY: 0.538 AC XY: 40004 AN XY: 74320

African (AFR) AF: 0.698 AC: 28961 AN: 41490

American (AMR) AF: 0.589 AC: 8999 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.447 AC: 1548 AN: 3466

East Asian (EAS) AF: 0.939 AC: 4879 AN: 5194

South Asian (SAS) AF: 0.786 AC: 3786 AN: 4818

European-Finnish (FIN) AF: 0.370 AC: 3907 AN: 10556

Middle Eastern (MID) AF: 0.595 AC: 175 AN: 294

European-Non Finnish (NFE) AF: 0.392 AC: 26635 AN: 67952

Other (OTH) AF: 0.528 AC: 1113 AN: 2108

Alfa AF: 0.518 Hom.: 19161

Bravo AF: 0.551

Asia WGS AF: 0.840 AC: 2914 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.27
CADD	Benign	16
DANN	Benign	0.70
PhyloP100		-0.068

Splicing

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

Other links and lift over

dbSNP: rs271738; hg19: chr1-234662890;