rs11247653

Variant names:

• chr1-27663109-A-G
• rs11247653
• ENST00000440492.2:n.225T>C

Variant summary

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

The ENST00000440492.2(LINC02574):​n.225T>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.325 in 152,110 control chromosomes in the GnomAD database, including 10,034 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 0.33 (10034 hom., cov: 32)
• Consequence: LINC02574 ENST00000440492.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0180
• Publications: 7 publications found

Genes affected

LINC02574 (HGNC:53746): (long intergenic non-protein coding RNA 2574)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.455 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
LINC02574	ENST00000440492.2	n.225T>C		non_coding_transcript_exon_variant	Exon 1 of 2	3
LINC02574	ENST00000681370.1	n.1195-929T>C		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.325 AC: 49464 AN: 151992 Hom.: 10038 Cov.: 32

Gnomad AFR AF: 0.0875

Gnomad AMI AF: 0.443

Gnomad AMR AF: 0.318

Gnomad ASJ AF: 0.412

Gnomad EAS AF: 0.190

Gnomad SAS AF: 0.420

Gnomad FIN AF: 0.388

Gnomad MID AF: 0.401

Gnomad NFE AF: 0.459

Gnomad OTH AF: 0.325

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

GnomAD4 genome AF: 0.325 AC: 49453 AN: 152110 Hom.: 10034 Cov.: 32 AF XY: 0.322 AC XY: 23912 AN XY: 74336

African (AFR) AF: 0.0873 AC: 3623 AN: 41522

American (AMR) AF: 0.318 AC: 4858 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.412 AC: 1431 AN: 3472

East Asian (EAS) AF: 0.189 AC: 979 AN: 5182

South Asian (SAS) AF: 0.422 AC: 2031 AN: 4818

European-Finnish (FIN) AF: 0.388 AC: 4103 AN: 10566

Middle Eastern (MID) AF: 0.397 AC: 116 AN: 292

European-Non Finnish (NFE) AF: 0.459 AC: 31225 AN: 67958

Other (OTH) AF: 0.324 AC: 684 AN: 2114

Alfa AF: 0.380 Hom.: 7958

Bravo AF: 0.305

Asia WGS AF: 0.325 AC: 1132 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	5.5
DANN	Benign	0.77
PhyloP100		0.018

Splicing

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

Other links and lift over

dbSNP: rs11247653; hg19: chr1-27989620;