9-90961551-C-T

Variant names:

• chr9-90961551-C-T
• rs426365
• ENST00000427745.1:n.130+3713G>A

Variant summary

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

The ENST00000427745.1(LINC02937):​n.130+3713G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.982 in 152,310 control chromosomes in the GnomAD database, including 73,492 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 0.98 (73492 hom., cov: 33)
• Consequence: LINC02937 ENST00000427745.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.76
• Publications: 0 publications found

Genes affected

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

LOC105379829 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.989 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000427745.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02937	ENST00000427745.1	TSL:3	n.130+3713G>A		intron	N/A
	LINC02937	ENST00000814915.1		n.273-4127G>A		intron	N/A
	LINC02937	ENST00000814918.1		n.153+3713G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.982 AC: 149426 AN: 152192 Hom.: 73433 Cov.: 33

Gnomad AFR AF: 0.997

Gnomad AMI AF: 0.965

Gnomad AMR AF: 0.938

Gnomad ASJ AF: 0.990

Gnomad EAS AF: 0.901

Gnomad SAS AF: 0.907

Gnomad FIN AF: 0.996

Gnomad MID AF: 0.981

Gnomad NFE AF: 0.992

Gnomad OTH AF: 0.979

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

GnomAD4 genome AF: 0.982 AC: 149545 AN: 152310 Hom.: 73492 Cov.: 33 AF XY: 0.979 AC XY: 72912 AN XY: 74458

African (AFR) AF: 0.997 AC: 41453 AN: 41576

American (AMR) AF: 0.938 AC: 14354 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.990 AC: 3437 AN: 3470

East Asian (EAS) AF: 0.901 AC: 4642 AN: 5154

South Asian (SAS) AF: 0.908 AC: 4380 AN: 4826

European-Finnish (FIN) AF: 0.996 AC: 10579 AN: 10626

Middle Eastern (MID) AF: 0.980 AC: 288 AN: 294

European-Non Finnish (NFE) AF: 0.992 AC: 67463 AN: 68038

Other (OTH) AF: 0.980 AC: 2071 AN: 2114

Alfa AF: 0.985 Hom.: 129912

Bravo AF: 0.980

Asia WGS AF: 0.912 AC: 3171 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.41
DANN	Benign	0.82
PhyloP100		-1.8

Splicing

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

Other links and lift over

dbSNP: rs426365; hg19: chr9-93723833;