14-38732715-G-C

Variant names:

• chr14-38732715-G-C
• rs10498349
• ENST00000776586.1:n.389+12429C>G

Variant summary

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

The ENST00000776586.1(LINC00639):​n.389+12429C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0941 in 152,150 control chromosomes in the GnomAD database, including 1,936 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 0.094 (1936 hom., cov: 32)
• Consequence: LINC00639 ENST00000776586.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.669
• Publications: 0 publications found

Genes affected

LINC00639 (HGNC:27502): (long intergenic non-protein coding RNA 639)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.292 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
LINC00639	ENST00000776586.1	n.389+12429C>G		intron_variant	Intron 4 of 4

Frequencies

GnomAD3 genomes AF: 0.0938 AC: 14264 AN: 152032 Hom.: 1921 Cov.: 32

Gnomad AFR AF: 0.296

Gnomad AMI AF: 0.0340

Gnomad AMR AF: 0.0542

Gnomad ASJ AF: 0.0173

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00642

Gnomad FIN AF: 0.00226

Gnomad MID AF: 0.0696

Gnomad NFE AF: 0.0134

Gnomad OTH AF: 0.0712

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

GnomAD4 genome AF: 0.0941 AC: 14321 AN: 152150 Hom.: 1936 Cov.: 32 AF XY: 0.0918 AC XY: 6831 AN XY: 74400

African (AFR) AF: 0.296 AC: 12270 AN: 41438

American (AMR) AF: 0.0541 AC: 827 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.0173 AC: 60 AN: 3470

East Asian (EAS) AF: 0.00 AC: 0 AN: 5182

South Asian (SAS) AF: 0.00601 AC: 29 AN: 4826

European-Finnish (FIN) AF: 0.00226 AC: 24 AN: 10610

Middle Eastern (MID) AF: 0.0748 AC: 22 AN: 294

European-Non Finnish (NFE) AF: 0.0134 AC: 909 AN: 68018

Other (OTH) AF: 0.0704 AC: 149 AN: 2116

Alfa AF: 0.00424 Hom.: 3

Bravo AF: 0.107

Asia WGS AF: 0.0260 AC: 92 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.6
DANN	Benign	0.46
PhyloP100		-0.67

Splicing

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

Other links and lift over

dbSNP: rs10498349; hg19: chr14-39201919;