rs1232027

Variant names:

• chr5-80619201-G-A
• rs1232027
• ENST00000515871.1:n.117+3207C>T

Variant summary

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

The ENST00000515871.1(LINC01337):​n.117+3207C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.318 in 152,110 control chromosomes in the GnomAD database, including 8,076 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 0.32 (8076 hom., cov: 32)
• Consequence: LINC01337 ENST00000515871.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.383
• Publications: 29 publications found

Genes affected

LINC01337 (HGNC:50546): (long intergenic non-protein coding RNA 1337)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.379 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01337	NR_125754.1	n.117+3207C>T		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01337	ENST00000515871.1	n.117+3207C>T		intron_variant	Intron 1 of 1	3

Frequencies

GnomAD3 genomes AF: 0.318 AC: 48381 AN: 151992 Hom.: 8069 Cov.: 32

Gnomad AFR AF: 0.384

Gnomad AMI AF: 0.327

Gnomad AMR AF: 0.263

Gnomad ASJ AF: 0.328

Gnomad EAS AF: 0.0158

Gnomad SAS AF: 0.336

Gnomad FIN AF: 0.261

Gnomad MID AF: 0.380

Gnomad NFE AF: 0.320

Gnomad OTH AF: 0.335

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

GnomAD4 genome AF: 0.318 AC: 48424 AN: 152110 Hom.: 8076 Cov.: 32 AF XY: 0.314 AC XY: 23351 AN XY: 74352

African (AFR) AF: 0.384 AC: 15931 AN: 41476

American (AMR) AF: 0.262 AC: 4008 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.328 AC: 1137 AN: 3468

East Asian (EAS) AF: 0.0160 AC: 83 AN: 5176

South Asian (SAS) AF: 0.336 AC: 1622 AN: 4832

European-Finnish (FIN) AF: 0.261 AC: 2760 AN: 10580

Middle Eastern (MID) AF: 0.388 AC: 114 AN: 294

European-Non Finnish (NFE) AF: 0.320 AC: 21766 AN: 67990

Other (OTH) AF: 0.335 AC: 705 AN: 2106

Alfa AF: 0.317 Hom.: 25974

Bravo AF: 0.317

Asia WGS AF: 0.205 AC: 717 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.1
DANN	Benign	0.17
PhyloP100		0.38

Splicing

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

Other links and lift over

dbSNP: rs1232027; hg19: chr5-79915020;