rs10505007

Variant names:

• chr8-101318165-A-C
• rs10505007
• ENST00000750988.1:n.677A>C

Your query was ambiguous. Multiple possible variants found:

• chr8-101318165-A-C
• chr8-101318165-A-G
• chr8-101318165-A-T

Variant summary

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

The ENST00000750988.1(ENSG00000297795):​n.677A>C variant causes a splice region, non coding transcript exon 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: 32)
• Consequence: ENSG00000297795 ENST00000750988.1 splice_region, non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.357
• Publications: 6 publications found

Genes affected

ENSG00000297795 (HGNC:):

LINC02844 (HGNC:54379): (long intergenic non-protein coding RNA 2844)

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=-0.89).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124901993	XM_047422525.1	c.217+4A>C		splice_region_variant, intron_variant	Intron 4 of 5		XP_047278481.1
LOC124901993	XM_047422526.1	c.217+4A>C		splice_region_variant, intron_variant	Intron 4 of 5		XP_047278482.1
LOC124901993	XR_007061034.1	n.1515+4A>C		splice_region_variant, intron_variant	Intron 5 of 6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000297795	ENST00000750988.1	n.677A>C		splice_region_variant, non_coding_transcript_exon_variant	Exon 5 of 7
ENSG00000297795	ENST00000750987.1	n.439+4A>C		splice_region_variant, intron_variant	Intron 4 of 5
ENSG00000297795	ENST00000750989.1	n.279+4A>C		splice_region_variant, intron_variant	Intron 3 of 4

Frequencies

GnomAD3 genomes Cov.: 32

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

GnomAD4 genome Cov.: 32

Alfa AF: 0.00 Hom.: 30621

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	6.1
DANN	Benign	0.71
PhyloP100		0.36

Splicing

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

Other links and lift over

dbSNP: rs10505007; hg19: chr8-102330393;