rs2994684

Variant names:

• chr10-31077342-T-A
• rs2994684
• ENST00000658872.1:n.323-28597T>A

Your query was ambiguous. Multiple possible variants found:

• chr10-31077342-T-A
• chr10-31077342-T-C
• chr10-31077342-T-G

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The ENST00000658872.1(LINC02664):​n.323-28597T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 30)
• Consequence: LINC02664 ENST00000658872.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00700
• Publications: 11 publications found

Genes affected

LINC02664 (HGNC:54150): (long intergenic non-protein coding RNA 2664)

LOC105376481 (HGNC:):

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105376481	XR_001747409.3	n.2795-28597T>A		intron_variant	Intron 1 of 2
LOC105376481	XR_001747410.3	n.2795-28597T>A		intron_variant	Intron 1 of 2
LOC105376481	XR_930796.3	n.904-28597T>A		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02664	ENST00000658872.1	n.323-28597T>A		intron_variant	Intron 1 of 2
LINC02664	ENST00000804994.1	n.91-28597T>A		intron_variant	Intron 1 of 3
LINC02664	ENST00000805304.1	n.212-28597T>A		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes Cov.: 30

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

GnomAD4 genome Cov.: 30

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	4.3
DANN	Benign	0.68
PhyloP100		0.0070

Splicing

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

Other links and lift over

dbSNP: rs2994684; hg19: chr10-31366271;