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 ENST00000814918.1(LINC02937):​n.261+3034T>G variant causes a 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 ENST00000814918.1 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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105379829	XR_001746828.2	n.243-2885T>G		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02937	ENST00000814918.1	n.261+3034T>G		intron_variant	Intron 2 of 2
LINC02937	ENST00000814921.1	n.248+3034T>G		intron_variant	Intron 2 of 2
LINC02937	ENST00000850628.1	n.243-4T>G		splice_region_variant, intron_variant	Intron 2 of 2
LINC02937	ENST00000850630.1	n.302+3034T>G		intron_variant	Intron 3 of 3

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 v4.3

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;