rs296648

Variant names:

• chr9-91066737-G-A
• rs296648
• NR_033912.1:n.1918C>T

Your query was ambiguous. Multiple possible variants found:

• chr9-91066737-G-A
• chr9-91066737-G-C

Variant summary

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

The NR_033912.1(LOC100129316):​n.1918C>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 0.0569 in 152,204 control chromosomes in the GnomAD database, including 318 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 0.057 (318 hom., cov: 33)
• Consequence: LOC100129316 NR_033912.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.647
• Publications: 0 publications found

Genes affected

LOC100129316 (HGNC:):

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=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0933 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC100129316	NR_033912.1	n.1918C>T		non_coding_transcript_exon_variant	Exon 3 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02937	ENST00000814739.1	n.450+31685C>T		intron_variant	Intron 2 of 2
LINC02937	ENST00000850629.1	n.84-59298C>T		intron_variant	Intron 1 of 7
LINC02937	ENST00000850630.1	n.104-59298C>T		intron_variant	Intron 1 of 3
LINC02937	ENST00000850631.1	n.130-59298C>T		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.0570 AC: 8667 AN: 152086 Hom.: 318 Cov.: 33

Gnomad AFR AF: 0.0952

Gnomad AMI AF: 0.0286

Gnomad AMR AF: 0.0272

Gnomad ASJ AF: 0.0498

Gnomad EAS AF: 0.0588

Gnomad SAS AF: 0.101

Gnomad FIN AF: 0.0677

Gnomad MID AF: 0.0696

Gnomad NFE AF: 0.0363

Gnomad OTH AF: 0.0546

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

GnomAD4 genome AF: 0.0569 AC: 8666 AN: 152204 Hom.: 318 Cov.: 33 AF XY: 0.0582 AC XY: 4335 AN XY: 74432

African (AFR) AF: 0.0950 AC: 3946 AN: 41520

American (AMR) AF: 0.0272 AC: 416 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0498 AC: 173 AN: 3472

East Asian (EAS) AF: 0.0589 AC: 305 AN: 5174

South Asian (SAS) AF: 0.101 AC: 484 AN: 4806

European-Finnish (FIN) AF: 0.0677 AC: 718 AN: 10606

Middle Eastern (MID) AF: 0.0680 AC: 20 AN: 294

European-Non Finnish (NFE) AF: 0.0363 AC: 2466 AN: 68014

Other (OTH) AF: 0.0531 AC: 112 AN: 2110

Alfa AF: 0.0430 Hom.: 502

Bravo AF: 0.0554

Asia WGS AF: 0.0730 AC: 253 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.20
DANN	Benign	0.52
PhyloP100		-0.65

Splicing

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

Other links and lift over

dbSNP: rs296648; hg19: chr9-93829019;