rs699213

Positions:

• chr10-90210931-C-G
• chr10-90210931-C-T

Variant summary

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

The ENST00000664430.1(LINC01374):​n.696-14108C>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 0.323 in 151,906 control chromosomes in the GnomAD database, including 8,750 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 0.32 (8750 hom., cov: 32)
• Consequence: LINC01374 ENST00000664430.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.408

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=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.468 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC01374	ENST00000664430.1	n.696-14108C>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.323 AC: 48963 AN: 151788 Hom.: 8747 Cov.: 32

Gnomad AFR AF: 0.474

Gnomad AMI AF: 0.311

Gnomad AMR AF: 0.267

Gnomad ASJ AF: 0.206

Gnomad EAS AF: 0.473

Gnomad SAS AF: 0.316

Gnomad FIN AF: 0.270

Gnomad MID AF: 0.297

Gnomad NFE AF: 0.247

Gnomad OTH AF: 0.311

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

GnomAD4 genome AF: 0.323 AC: 48992 AN: 151906 Hom.: 8750 Cov.: 32 AF XY: 0.324 AC XY: 24055 AN XY: 74212

Gnomad4 AFR AF: 0.474

Gnomad4 AMR AF: 0.267

Gnomad4 ASJ AF: 0.206

Gnomad4 EAS AF: 0.474

Gnomad4 SAS AF: 0.316

Gnomad4 FIN AF: 0.270

Gnomad4 NFE AF: 0.247

Gnomad4 OTH AF: 0.308

Alfa AF: 0.289 Hom.: 843

Bravo AF: 0.328

Asia WGS AF: 0.370 AC: 1290 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.2
DANN	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs699213; hg19: chr10-91970688;