rs1998643

Positions:

• chr10-89859235-A-G

Variant summary

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

The NR_149080.1(LINC01374):​n.102+5228A>G variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.153 in 152,062 control chromosomes in the GnomAD database, including 1,944 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 0.15 (1944 hom., cov: 32)
• Consequence: LINC01374 NR_149080.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.786

Genes affected

LINC01374 (HGNC:50631): (long intergenic non-protein coding RNA 1374)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.352 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC01374	NR_149080.1	n.102+5228A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC01374	ENST00000664430.1	n.413+5228A>G		intron_variant, non_coding_transcript_variant
LINC01374	ENST00000629067.1	n.102+5228A>G		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.153 AC: 23274 AN: 151944 Hom.: 1939 Cov.: 32

Gnomad AFR AF: 0.142

Gnomad AMI AF: 0.157

Gnomad AMR AF: 0.115

Gnomad ASJ AF: 0.201

Gnomad EAS AF: 0.0699

Gnomad SAS AF: 0.366

Gnomad FIN AF: 0.197

Gnomad MID AF: 0.178

Gnomad NFE AF: 0.150

Gnomad OTH AF: 0.150

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

GnomAD4 genome AF: 0.153 AC: 23285 AN: 152062 Hom.: 1944 Cov.: 32 AF XY: 0.158 AC XY: 11760 AN XY: 74338

Gnomad4 AFR AF: 0.142

Gnomad4 AMR AF: 0.115

Gnomad4 ASJ AF: 0.201

Gnomad4 EAS AF: 0.0693

Gnomad4 SAS AF: 0.366

Gnomad4 FIN AF: 0.197

Gnomad4 NFE AF: 0.150

Gnomad4 OTH AF: 0.154

Alfa AF: 0.148 Hom.: 2854

Bravo AF: 0.138

Asia WGS AF: 0.258 AC: 890 AN: 3460

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	3.6
DANN	Benign	0.87

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1998643; hg19: chr10-91618992;