chr9-91090533-G-T

Position:

• chr9-91090533-G-T

Variant summary

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

The NR_184105.1(LINC02937):​n.2294+7889C>A variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.364 in 152,032 control chromosomes in the GnomAD database, including 10,621 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 0.36 (10621 hom., cov: 32)
• Consequence: LINC02937 NR_184105.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.53

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.472 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC02937	NR_184105.1	n.2294+7889C>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000686463.1	n.401+7889C>A		intron_variant, non_coding_transcript_variant
	ENST00000663149.1	n.966+7889C>A		intron_variant, non_coding_transcript_variant
	ENST00000666264.1	n.463-621C>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.364 AC: 55295 AN: 151914 Hom.: 10619 Cov.: 32

Gnomad AFR AF: 0.468

Gnomad AMI AF: 0.243

Gnomad AMR AF: 0.350

Gnomad ASJ AF: 0.441

Gnomad EAS AF: 0.488

Gnomad SAS AF: 0.463

Gnomad FIN AF: 0.303

Gnomad MID AF: 0.427

Gnomad NFE AF: 0.294

Gnomad OTH AF: 0.381

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

GnomAD4 genome AF: 0.364 AC: 55336 AN: 152032 Hom.: 10621 Cov.: 32 AF XY: 0.366 AC XY: 27176 AN XY: 74312

Gnomad4 AFR AF: 0.468

Gnomad4 AMR AF: 0.350

Gnomad4 ASJ AF: 0.441

Gnomad4 EAS AF: 0.487

Gnomad4 SAS AF: 0.463

Gnomad4 FIN AF: 0.303

Gnomad4 NFE AF: 0.294

Gnomad4 OTH AF: 0.380

Alfa AF: 0.317 Hom.: 7784

Bravo AF: 0.373

Asia WGS AF: 0.500 AC: 1737 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.15
DANN	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs430794; hg19: chr9-93852815;