13-38686756-C-T

Variant names:

• chr13-38686756-C-T
• rs55860060
• NR_126377.1:n.-81G>A

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NR_126377.1(LINC00437):​n.-81G>A variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.216 in 151,984 control chromosomes in the GnomAD database, including 4,266 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.22 (4266 hom., cov: 32)
• Consequence: LINC00437 NR_126377.1 upstream_gene
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.215

Genes affected

LINC00437 (HGNC:42772): (long intergenic non-protein coding RNA 437)

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BP6: Variant 13-38686756-C-T is Benign according to our data. Variant chr13-38686756-C-T is described in ClinVar as [Benign]. Clinvar id is 1287018.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.352 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC00437	NR_126377.1	n.-81G>A		upstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.216 AC: 32866 AN: 151866 Hom.: 4269 Cov.: 32

Gnomad AFR AF: 0.0733

Gnomad AMI AF: 0.274

Gnomad AMR AF: 0.285

Gnomad ASJ AF: 0.247

Gnomad EAS AF: 0.365

Gnomad SAS AF: 0.267

Gnomad FIN AF: 0.316

Gnomad MID AF: 0.253

Gnomad NFE AF: 0.255

Gnomad OTH AF: 0.219

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

GnomAD4 genome AF: 0.216 AC: 32869 AN: 151984 Hom.: 4266 Cov.: 32 AF XY: 0.221 AC XY: 16414 AN XY: 74270

Gnomad4 AFR AF: 0.0733

Gnomad4 AMR AF: 0.285

Gnomad4 ASJ AF: 0.247

Gnomad4 EAS AF: 0.366

Gnomad4 SAS AF: 0.266

Gnomad4 FIN AF: 0.316

Gnomad4 NFE AF: 0.255

Gnomad4 OTH AF: 0.220

Alfa AF: 0.127 Hom.: 235

Bravo AF: 0.208

Asia WGS AF: 0.317 AC: 1102 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Nov 11, 2018

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	1.5
DANN	Benign	0.81

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs55860060; hg19: chr13-39260893;