rs10148969

Variant names:

• chr14-90502030-C-T
• rs10148969
• ENST00000849844.1:n.430-3734C>T

Variant summary

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

The ENST00000849844.1(LINC00642):​n.430-3734C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.416 in 151,802 control chromosomes in the GnomAD database, including 13,742 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 0.42 (13742 hom., cov: 31)
• Consequence: LINC00642 ENST00000849844.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.145
• Publications: 1 publications found

Genes affected

LINC00642 (HGNC:44293): (long intergenic non-protein coding RNA 642)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.68 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000849844.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC00642	ENST00000849844.1		n.430-3734C>T		intron	N/A
	LINC00642	ENST00000849845.1		n.318-3734C>T		intron	N/A
	LINC00642	ENST00000849846.1		n.328-3734C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.416 AC: 63106 AN: 151686 Hom.: 13737 Cov.: 31

Gnomad AFR AF: 0.351

Gnomad AMI AF: 0.165

Gnomad AMR AF: 0.554

Gnomad ASJ AF: 0.473

Gnomad EAS AF: 0.699

Gnomad SAS AF: 0.567

Gnomad FIN AF: 0.410

Gnomad MID AF: 0.481

Gnomad NFE AF: 0.393

Gnomad OTH AF: 0.437

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

GnomAD4 genome AF: 0.416 AC: 63145 AN: 151802 Hom.: 13742 Cov.: 31 AF XY: 0.425 AC XY: 31547 AN XY: 74178

African (AFR) AF: 0.351 AC: 14532 AN: 41412

American (AMR) AF: 0.555 AC: 8468 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.473 AC: 1641 AN: 3470

East Asian (EAS) AF: 0.699 AC: 3592 AN: 5140

South Asian (SAS) AF: 0.566 AC: 2719 AN: 4808

European-Finnish (FIN) AF: 0.410 AC: 4328 AN: 10544

Middle Eastern (MID) AF: 0.490 AC: 142 AN: 290

European-Non Finnish (NFE) AF: 0.393 AC: 26654 AN: 67858

Other (OTH) AF: 0.436 AC: 919 AN: 2110

Alfa AF: 0.408 Hom.: 6793

Bravo AF: 0.422

Asia WGS AF: 0.591 AC: 2054 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	3.5
DANN	Benign	0.71
PhyloP100		0.14

Splicing

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

Other links and lift over

dbSNP: rs10148969; hg19: chr14-90968374;