rs7071717

Positions:

• chr10-90058530-A-G

Variant summary

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

The ENST00000664430.1(LINC01374):​n.549-41762A>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 0.0609 in 152,272 control chromosomes in the GnomAD database, including 446 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 0.061 (446 hom., cov: 33)
• Consequence: LINC01374 ENST00000664430.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.312

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=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.122 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.549-41762A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0608 AC: 9254 AN: 152154 Hom.: 442 Cov.: 33

Gnomad AFR AF: 0.125

Gnomad AMI AF: 0.0844

Gnomad AMR AF: 0.0364

Gnomad ASJ AF: 0.0164

Gnomad EAS AF: 0.00250

Gnomad SAS AF: 0.0265

Gnomad FIN AF: 0.0127

Gnomad MID AF: 0.0190

Gnomad NFE AF: 0.0443

Gnomad OTH AF: 0.0507

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

GnomAD4 genome AF: 0.0609 AC: 9267 AN: 152272 Hom.: 446 Cov.: 33 AF XY: 0.0579 AC XY: 4314 AN XY: 74470

Gnomad4 AFR AF: 0.125

Gnomad4 AMR AF: 0.0364

Gnomad4 ASJ AF: 0.0164

Gnomad4 EAS AF: 0.00270

Gnomad4 SAS AF: 0.0270

Gnomad4 FIN AF: 0.0127

Gnomad4 NFE AF: 0.0443

Gnomad4 OTH AF: 0.0497

Alfa AF: 0.0504 Hom.: 37

Bravo AF: 0.0650

Asia WGS AF: 0.0290 AC: 103 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.88
DANN	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7071717; hg19: chr10-91818287;