9-91166134-C-T

Variant names:

• chr9-91166134-C-T
• rs4743820
• ENST00000659376.2:n.3885C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000659376.2(LINC00484):​n.3885C>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 ENST00000659376.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.988
• Publications: 46 publications found

Genes affected

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

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

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
LINC00484	NR_135306.1	n.161-16335C>T		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC00484	ENST00000659376.2	n.3885C>T		non_coding_transcript_exon_variant	Exon 2 of 2
LINC00484	ENST00000439438.1	n.161-16335C>T		intron_variant	Intron 2 of 2	3
LINC02937	ENST00000667274.1	n.202+46711G>A		intron_variant	Intron 1 of 2

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

African (AFR) AF: 0.397 AC: 16408 AN: 41356

American (AMR) AF: 0.735 AC: 11223 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.648 AC: 2247 AN: 3468

East Asian (EAS) AF: 0.659 AC: 3401 AN: 5164

South Asian (SAS) AF: 0.677 AC: 3265 AN: 4820

European-Finnish (FIN) AF: 0.647 AC: 6799 AN: 10502

Middle Eastern (MID) AF: 0.656 AC: 193 AN: 294

European-Non Finnish (NFE) AF: 0.705 AC: 47891 AN: 67934

Other (OTH) AF: 0.663 AC: 1397 AN: 2106

Alfa AF: 0.662 Hom.: 69624

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
PhyloP100		-0.99

Splicing

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

Other links and lift over

dbSNP: rs4743820; hg19: chr9-93928416;