9-91166134-C-T

Position:

• chr9-91166134-C-T

Variant summary

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

The ENST00000659376.1(LINC00484):​n.3852C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.615 in 151,830 control chromosomes in the GnomAD database, including 30,202 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 0.62 (30202 hom., cov: 30)
• Consequence: LINC00484 ENST00000659376.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.988

Genes affected

LINC00484 (HGNC:27862): (long intergenic non-protein coding RNA 484)

LINC02937 (HGNC:55942): (long intergenic non-protein coding RNA 2937)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.723 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC00484	NR_135306.1	n.161-16335C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC00484	ENST00000659376.1	n.3852C>T		non_coding_transcript_exon_variant	2/2
LINC00484	ENST00000439438.1	n.161-16335C>T		intron_variant, non_coding_transcript_variant		3
LINC02937	ENST00000667274.1	n.202+46711G>A		intron_variant, non_coding_transcript_variant
LINC00484	ENST00000668360.2	n.157-16335C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.615 AC: 93365 AN: 151712 Hom.: 30183 Cov.: 30

Gnomad AFR AF: 0.396

Gnomad AMI AF: 0.664

Gnomad AMR AF: 0.735

Gnomad ASJ AF: 0.648

Gnomad EAS AF: 0.659

Gnomad SAS AF: 0.676

Gnomad FIN AF: 0.647

Gnomad MID AF: 0.665

Gnomad NFE AF: 0.705

Gnomad OTH AF: 0.663

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

GnomAD4 genome AF: 0.615 AC: 93430 AN: 151830 Hom.: 30202 Cov.: 30 AF XY: 0.616 AC XY: 45709 AN XY: 74178

Gnomad4 AFR AF: 0.397

Gnomad4 AMR AF: 0.735

Gnomad4 ASJ AF: 0.648

Gnomad4 EAS AF: 0.659

Gnomad4 SAS AF: 0.677

Gnomad4 FIN AF: 0.647

Gnomad4 NFE AF: 0.705

Gnomad4 OTH AF: 0.663

Alfa AF: 0.655 Hom.: 11963

Bravo AF: 0.609

Asia WGS AF: 0.645 AC: 2245 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.75
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: rs4743820; hg19: chr9-93928416;