14-51337371-T-G

Variant names:

• chr14-51337371-T-G
• rs11625012
• ENST00000554409.2:n.274+3807T>G

Variant summary

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

The ENST00000554409.2(LINC00640):​n.274+3807T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.254 in 152,218 control chromosomes in the GnomAD database, including 6,128 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 0.25 (6128 hom., cov: 33)
• Consequence: LINC00640 ENST00000554409.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.145
• Publications: 4 publications found

Genes affected

LINC00640 (HGNC:44291): (long intergenic non-protein coding RNA 640)

ENSG00000258942 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.35 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000554409.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC00640	NR_038358.1		n.172+3807T>G		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC00640	ENST00000554409.2	TSL:3	n.274+3807T>G		intron	N/A
	LINC00640	ENST00000556479.6	TSL:2	n.497+3807T>G		intron	N/A
	LINC00640	ENST00000557295.1	TSL:5	n.23+3807T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.254 AC: 38633 AN: 152100 Hom.: 6128 Cov.: 33

Gnomad AFR AF: 0.0754

Gnomad AMI AF: 0.503

Gnomad AMR AF: 0.297

Gnomad ASJ AF: 0.398

Gnomad EAS AF: 0.102

Gnomad SAS AF: 0.217

Gnomad FIN AF: 0.269

Gnomad MID AF: 0.234

Gnomad NFE AF: 0.354

Gnomad OTH AF: 0.284

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

GnomAD4 genome AF: 0.254 AC: 38645 AN: 152218 Hom.: 6128 Cov.: 33 AF XY: 0.250 AC XY: 18596 AN XY: 74430

African (AFR) AF: 0.0753 AC: 3132 AN: 41568

American (AMR) AF: 0.297 AC: 4550 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.398 AC: 1380 AN: 3470

East Asian (EAS) AF: 0.103 AC: 534 AN: 5180

South Asian (SAS) AF: 0.217 AC: 1047 AN: 4824

European-Finnish (FIN) AF: 0.269 AC: 2846 AN: 10588

Middle Eastern (MID) AF: 0.231 AC: 68 AN: 294

European-Non Finnish (NFE) AF: 0.354 AC: 24033 AN: 67978

Other (OTH) AF: 0.283 AC: 597 AN: 2110

Alfa AF: 0.296 Hom.: 4232

Bravo AF: 0.247

Asia WGS AF: 0.183 AC: 634 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	6.0
DANN	Benign	0.80
PhyloP100		-0.14

Splicing

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

Other links and lift over

dbSNP: rs11625012; hg19: chr14-51804089;