chr14-51337371-T-G

Position:

• chr14-51337371-T-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000556479.6(LINC00640):​n.497+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 ENST00000556479.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.145

Genes affected

LINC00640 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC00640	NR_038358.1	n.172+3807T>G		intron_variant
LOC124900595	XR_943854.3	n.83-1182A>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC00640	ENST00000554409.1	n.24+3807T>G		intron_variant		3
LINC00640	ENST00000556479.6	n.497+3807T>G		intron_variant		2
LINC00640	ENST00000557295.1	n.23+3807T>G		intron_variant		5

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

Gnomad4 AFR AF: 0.0753

Gnomad4 AMR AF: 0.297

Gnomad4 ASJ AF: 0.398

Gnomad4 EAS AF: 0.103

Gnomad4 SAS AF: 0.217

Gnomad4 FIN AF: 0.269

Gnomad4 NFE AF: 0.354

Gnomad4 OTH AF: 0.283

Alfa AF: 0.294 Hom.: 3762

Bravo AF: 0.247

Asia WGS AF: 0.183 AC: 634 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11625012; hg19: chr14-51804089;