rs4748940

Variant names:

• chr10-7466537-A-G
• rs4748940
• NR_184108.1:n.1230T>C

Variant summary

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

The NR_184108.1(LINC02642):​n.1230T>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.233 in 152,166 control chromosomes in the GnomAD database, including 4,396 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 0.23 (4396 hom., cov: 32)
• Consequence: LINC02642 NR_184108.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.114
• Publications: 5 publications found

Genes affected

LINC02642 (HGNC:54124): (long intergenic non-protein coding RNA 2642)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.275 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02642	NR_184108.1	n.1230T>C		non_coding_transcript_exon_variant	Exon 3 of 3
LINC02642	NR_184114.1	n.3505T>C		non_coding_transcript_exon_variant	Exon 3 of 3
LINC02642	NR_184125.1	n.1385T>C		non_coding_transcript_exon_variant	Exon 4 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02642	ENST00000420395.1	n.322+860T>C		intron_variant	Intron 3 of 3	3
LINC02642	ENST00000660269.1	n.542+860T>C		intron_variant	Intron 4 of 4
LINC02642	ENST00000670632.2	n.476+860T>C		intron_variant	Intron 4 of 4

Frequencies

GnomAD3 genomes AF: 0.233 AC: 35427 AN: 152048 Hom.: 4404 Cov.: 32

Gnomad AFR AF: 0.169

Gnomad AMI AF: 0.309

Gnomad AMR AF: 0.195

Gnomad ASJ AF: 0.268

Gnomad EAS AF: 0.174

Gnomad SAS AF: 0.213

Gnomad FIN AF: 0.264

Gnomad MID AF: 0.294

Gnomad NFE AF: 0.279

Gnomad OTH AF: 0.237

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

GnomAD4 genome AF: 0.233 AC: 35421 AN: 152166 Hom.: 4396 Cov.: 32 AF XY: 0.230 AC XY: 17143 AN XY: 74384

African (AFR) AF: 0.169 AC: 6999 AN: 41518

American (AMR) AF: 0.195 AC: 2975 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.268 AC: 931 AN: 3470

East Asian (EAS) AF: 0.174 AC: 901 AN: 5190

South Asian (SAS) AF: 0.212 AC: 1025 AN: 4828

European-Finnish (FIN) AF: 0.264 AC: 2793 AN: 10572

Middle Eastern (MID) AF: 0.286 AC: 84 AN: 294

European-Non Finnish (NFE) AF: 0.279 AC: 18934 AN: 67982

Other (OTH) AF: 0.236 AC: 497 AN: 2110

Alfa AF: 0.262 Hom.: 2604

Bravo AF: 0.226

Asia WGS AF: 0.192 AC: 666 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	1.7
DANN	Benign	0.60
PhyloP100		0.11

Splicing

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

Other links and lift over

dbSNP: rs4748940; hg19: chr10-7508499;