14-47871538-A-C

Variant names:

• chr14-47871538-A-C
• rs1451928
• ENST00000802535.1:n.243+29086T>G

Variant summary

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

The ENST00000802535.1(LINC00648):​n.243+29086T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.208 in 152,138 control chromosomes in the GnomAD database, including 3,877 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 0.21 (3877 hom., cov: 32)
• Consequence: LINC00648 ENST00000802535.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.954
• Publications: 8 publications found

Genes affected

LINC00648 (HGNC:44302): (long intergenic non-protein coding RNA 648)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.38 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
LINC00648	ENST00000802535.1	n.243+29086T>G		intron_variant	Intron 2 of 3
LINC00648	ENST00000802536.1	n.129+29988T>G		intron_variant	Intron 1 of 2
LINC00648	ENST00000802537.1	n.239+29086T>G		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.208 AC: 31688 AN: 152020 Hom.: 3875 Cov.: 32

Gnomad AFR AF: 0.116

Gnomad AMI AF: 0.192

Gnomad AMR AF: 0.324

Gnomad ASJ AF: 0.235

Gnomad EAS AF: 0.220

Gnomad SAS AF: 0.396

Gnomad FIN AF: 0.235

Gnomad MID AF: 0.199

Gnomad NFE AF: 0.220

Gnomad OTH AF: 0.197

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

GnomAD4 genome AF: 0.208 AC: 31701 AN: 152138 Hom.: 3877 Cov.: 32 AF XY: 0.214 AC XY: 15891 AN XY: 74374

African (AFR) AF: 0.116 AC: 4827 AN: 41528

American (AMR) AF: 0.324 AC: 4955 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.235 AC: 816 AN: 3470

East Asian (EAS) AF: 0.221 AC: 1144 AN: 5180

South Asian (SAS) AF: 0.395 AC: 1903 AN: 4816

European-Finnish (FIN) AF: 0.235 AC: 2489 AN: 10578

Middle Eastern (MID) AF: 0.197 AC: 58 AN: 294

European-Non Finnish (NFE) AF: 0.220 AC: 14922 AN: 67968

Other (OTH) AF: 0.195 AC: 412 AN: 2112

Alfa AF: 0.191 Hom.: 1467

Bravo AF: 0.208

Asia WGS AF: 0.278 AC: 965 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	4.6
DANN	Benign	0.88
PhyloP100		0.95

Splicing

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

Other links and lift over

dbSNP: rs1451928; hg19: chr14-48340741;