rs1675306

Variant names:

• chr9-90934941-A-C
• rs1675306
• ENST00000814918.1:n.261+3034T>G

Your query was ambiguous. Multiple possible variants found:

• chr9-90934941-A-C
• chr9-90934941-A-G
• chr9-90934941-A-T

Variant summary

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

The ENST00000850628.1(LINC02937):​n.243-4T>G variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.944 in 152,312 control chromosomes in the GnomAD database, including 68,168 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 0.94 (68168 hom., cov: 34)
• Consequence: LINC02937 ENST00000850628.1 splice_region, intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.355
• Publications: 3 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=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.983 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000850628.1. 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	ENST00000814918.1		n.261+3034T>G		intron	N/A
	LINC02937	ENST00000814921.1		n.248+3034T>G		intron	N/A
	LINC02937	ENST00000850628.1		n.243-4T>G		splice_region intron	N/A

Frequencies

GnomAD3 genomes AF: 0.944 AC: 143729 AN: 152194 Hom.: 68133 Cov.: 34

Gnomad AFR AF: 0.869

Gnomad AMI AF: 0.965

Gnomad AMR AF: 0.922

Gnomad ASJ AF: 0.991

Gnomad EAS AF: 0.897

Gnomad SAS AF: 0.928

Gnomad FIN AF: 0.995

Gnomad MID AF: 0.972

Gnomad NFE AF: 0.989

Gnomad OTH AF: 0.957

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

GnomAD4 genome AF: 0.944 AC: 143819 AN: 152312 Hom.: 68168 Cov.: 34 AF XY: 0.943 AC XY: 70220 AN XY: 74482

African (AFR) AF: 0.869 AC: 36091 AN: 41554

American (AMR) AF: 0.922 AC: 14106 AN: 15304

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

East Asian (EAS) AF: 0.897 AC: 4643 AN: 5178

South Asian (SAS) AF: 0.927 AC: 4473 AN: 4824

European-Finnish (FIN) AF: 0.995 AC: 10572 AN: 10622

Middle Eastern (MID) AF: 0.976 AC: 287 AN: 294

European-Non Finnish (NFE) AF: 0.989 AC: 67307 AN: 68042

Other (OTH) AF: 0.957 AC: 2022 AN: 2112

Alfa AF: 0.976 Hom.: 67466

Bravo AF: 0.941

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.73
DANN	Benign	0.60
PhyloP100		-0.35

Splicing

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

Other links and lift over

dbSNP: rs1675306; hg19: chr9-93697223;