rs11185978

Positions:

• chr10-90029031-T-G

Variant summary

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

The ENST00000664430.1(LINC01374):​n.549-71261T>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 0.0509 in 152,208 control chromosomes in the GnomAD database, including 291 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 0.051 (291 hom., cov: 32)
• Consequence: LINC01374 ENST00000664430.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.203

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=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.091 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.549-71261T>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0508 AC: 7730 AN: 152090 Hom.: 290 Cov.: 32

Gnomad AFR AF: 0.0935

Gnomad AMI AF: 0.0835

Gnomad AMR AF: 0.0322

Gnomad ASJ AF: 0.0303

Gnomad EAS AF: 0.00327

Gnomad SAS AF: 0.0102

Gnomad FIN AF: 0.0123

Gnomad MID AF: 0.0190

Gnomad NFE AF: 0.0426

Gnomad OTH AF: 0.0407

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

GnomAD4 genome AF: 0.0509 AC: 7741 AN: 152208 Hom.: 291 Cov.: 32 AF XY: 0.0479 AC XY: 3569 AN XY: 74432

Gnomad4 AFR AF: 0.0935

Gnomad4 AMR AF: 0.0321

Gnomad4 ASJ AF: 0.0303

Gnomad4 EAS AF: 0.00347

Gnomad4 SAS AF: 0.0106

Gnomad4 FIN AF: 0.0123

Gnomad4 NFE AF: 0.0426

Gnomad4 OTH AF: 0.0398

Alfa AF: 0.0438 Hom.: 22

Bravo AF: 0.0542

Asia WGS AF: 0.0160 AC: 56 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.2
DANN	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11185978; hg19: chr10-91788788;