chr9-90981938-A-G

Variant names:

• chr9-90981938-A-G
• rs296720
• ENST00000814915.1:n.199-4814T>C

Variant summary

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

The ENST00000814915.1(LINC02937):​n.199-4814T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.98 in 152,342 control chromosomes in the GnomAD database, including 73,245 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 (73245 hom., cov: 34)
• Consequence: LINC02937 ENST00000814915.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.288
• Publications: 1 publications found

Genes affected

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=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.989 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02937	ENST00000814915.1	n.199-4814T>C		intron_variant	Intron 2 of 3
LINC02937	ENST00000814916.1	n.279-4814T>C		intron_variant	Intron 2 of 3
LINC02937	ENST00000814917.1	n.180-4814T>C		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.980 AC: 149164 AN: 152224 Hom.: 73187 Cov.: 34

Gnomad AFR AF: 0.997

Gnomad AMI AF: 0.965

Gnomad AMR AF: 0.938

Gnomad ASJ AF: 0.991

Gnomad EAS AF: 0.866

Gnomad SAS AF: 0.902

Gnomad FIN AF: 0.995

Gnomad MID AF: 0.981

Gnomad NFE AF: 0.991

Gnomad OTH AF: 0.976

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

GnomAD4 genome AF: 0.980 AC: 149281 AN: 152342 Hom.: 73245 Cov.: 34 AF XY: 0.977 AC XY: 72797 AN XY: 74492

African (AFR) AF: 0.997 AC: 41454 AN: 41586

American (AMR) AF: 0.938 AC: 14343 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.991 AC: 3440 AN: 3472

East Asian (EAS) AF: 0.866 AC: 4485 AN: 5178

South Asian (SAS) AF: 0.902 AC: 4351 AN: 4824

European-Finnish (FIN) AF: 0.995 AC: 10570 AN: 10620

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

European-Non Finnish (NFE) AF: 0.991 AC: 67407 AN: 68044

Other (OTH) AF: 0.976 AC: 2063 AN: 2114

Alfa AF: 0.990 Hom.: 8676

Bravo AF: 0.979

Asia WGS AF: 0.896 AC: 3116 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.8
DANN	Benign	0.36
PhyloP100		0.29

Splicing

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

Other links and lift over

dbSNP: rs296720; hg19: chr9-93744220;