chr13-111589370-G-A

Variant names:

• chr13-111589370-G-A
• rs4773396
• ENST00000607406.1:n.1170G>A

Variant summary

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

The ENST00000607406.1(LINC02337):​n.1170G>A 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 0.438 in 152,048 control chromosomes in the GnomAD database, including 16,005 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 0.44 (15996 hom., cov: 32)
  • Exomes 𝑓: 0.52 (9 hom.)
• Consequence: LINC02337 ENST00000607406.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0340
• Publications: 2 publications found

Genes affected

LINC02337 (HGNC:53257): (long intergenic non-protein coding RNA 2337)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.521 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
LINC02337	ENST00000607406.1	n.1170G>A		non_coding_transcript_exon_variant	Exon 1 of 1	6
LINC02337	ENST00000375713.1	n.54+1026G>A		intron_variant	Intron 1 of 3	5
LINC02337	ENST00000830127.1	n.144+1026G>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.438 AC: 66459 AN: 151876 Hom.: 15976 Cov.: 32

Gnomad AFR AF: 0.220

Gnomad AMI AF: 0.576

Gnomad AMR AF: 0.468

Gnomad ASJ AF: 0.458

Gnomad EAS AF: 0.530

Gnomad SAS AF: 0.429

Gnomad FIN AF: 0.613

Gnomad MID AF: 0.440

Gnomad NFE AF: 0.526

Gnomad OTH AF: 0.448

GnomAD4 exome AF: 0.518 AC: 29 AN: 56 Hom.: 9 Cov.: 0 AF XY: 0.565 AC XY: 26 AN XY: 46

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AF: 0.00 AC: 0 AN: 2

South Asian (SAS) AF: 0.00 AC: 0 AN: 2

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AF: 1.00 AC: 2 AN: 2

European-Non Finnish (NFE) AF: 0.568 AC: 25 AN: 44

Other (OTH) AF: 0.333 AC: 2 AN: 6

GnomAD4 genome AF: 0.438 AC: 66510 AN: 151992 Hom.: 15996 Cov.: 32 AF XY: 0.442 AC XY: 32847 AN XY: 74298

African (AFR) AF: 0.220 AC: 9139 AN: 41468

American (AMR) AF: 0.469 AC: 7169 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.458 AC: 1588 AN: 3470

East Asian (EAS) AF: 0.531 AC: 2738 AN: 5158

South Asian (SAS) AF: 0.431 AC: 2077 AN: 4818

European-Finnish (FIN) AF: 0.613 AC: 6472 AN: 10554

Middle Eastern (MID) AF: 0.442 AC: 129 AN: 292

European-Non Finnish (NFE) AF: 0.526 AC: 35729 AN: 67932

Other (OTH) AF: 0.449 AC: 946 AN: 2108

Alfa AF: 0.472 Hom.: 3006

Bravo AF: 0.420

Asia WGS AF: 0.458 AC: 1592 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	4.4
DANN	Benign	0.39
PhyloP100		0.034

Splicing

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

Other links and lift over

dbSNP: rs4773396; hg19: chr13-112241717;