10-90202913-A-G

Position:

• chr10-90202913-A-G

Variant summary

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

The ENST00000664430.1(LINC01374):​n.696-22126A>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 0.33 in 151,742 control chromosomes in the GnomAD database, including 9,134 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 0.33 (9134 hom., cov: 32)
• Consequence: LINC01374 ENST00000664430.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.876

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 = 0.476 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC01374	ENST00000664430.1	n.696-22126A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.330 AC: 50032 AN: 151624 Hom.: 9132 Cov.: 32

Gnomad AFR AF: 0.482

Gnomad AMI AF: 0.338

Gnomad AMR AF: 0.274

Gnomad ASJ AF: 0.208

Gnomad EAS AF: 0.472

Gnomad SAS AF: 0.325

Gnomad FIN AF: 0.274

Gnomad MID AF: 0.307

Gnomad NFE AF: 0.255

Gnomad OTH AF: 0.315

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

GnomAD4 genome AF: 0.330 AC: 50061 AN: 151742 Hom.: 9134 Cov.: 32 AF XY: 0.331 AC XY: 24556 AN XY: 74176

Gnomad4 AFR AF: 0.481

Gnomad4 AMR AF: 0.274

Gnomad4 ASJ AF: 0.208

Gnomad4 EAS AF: 0.473

Gnomad4 SAS AF: 0.326

Gnomad4 FIN AF: 0.274

Gnomad4 NFE AF: 0.255

Gnomad4 OTH AF: 0.312

Alfa AF: 0.266 Hom.: 9529

Bravo AF: 0.335

Asia WGS AF: 0.380 AC: 1324 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	3.9
DANN	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2250245; hg19: chr10-91962670;