8-101318165-A-G

Variant names:

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

Variant summary

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

The ENST00000750988.1(ENSG00000297795):​n.677A>G variant causes a splice region, non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.346 in 151,962 control chromosomes in the GnomAD database, including 9,191 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 0.35 (9191 hom., 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: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.369 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124901993	XM_047422525.1	c.217+4A>G		splice_region_variant, intron_variant	Intron 4 of 5		XP_047278481.1
LOC124901993	XM_047422526.1	c.217+4A>G		splice_region_variant, intron_variant	Intron 4 of 5		XP_047278482.1
LOC124901993	XR_007061034.1	n.1515+4A>G		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>G		splice_region_variant, non_coding_transcript_exon_variant	Exon 5 of 7
ENSG00000297795	ENST00000750987.1	n.439+4A>G		splice_region_variant, intron_variant	Intron 4 of 5
ENSG00000297795	ENST00000750989.1	n.279+4A>G		splice_region_variant, intron_variant	Intron 3 of 4

Frequencies

GnomAD3 genomes AF: 0.347 AC: 52628 AN: 151844 Hom.: 9189 Cov.: 32

Gnomad AFR AF: 0.325

Gnomad AMI AF: 0.444

Gnomad AMR AF: 0.300

Gnomad ASJ AF: 0.363

Gnomad EAS AF: 0.233

Gnomad SAS AF: 0.384

Gnomad FIN AF: 0.402

Gnomad MID AF: 0.347

Gnomad NFE AF: 0.366

Gnomad OTH AF: 0.329

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

GnomAD4 genome AF: 0.346 AC: 52634 AN: 151962 Hom.: 9191 Cov.: 32 AF XY: 0.345 AC XY: 25636 AN XY: 74254

African (AFR) AF: 0.325 AC: 13455 AN: 41452

American (AMR) AF: 0.300 AC: 4582 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.363 AC: 1256 AN: 3464

East Asian (EAS) AF: 0.232 AC: 1196 AN: 5166

South Asian (SAS) AF: 0.383 AC: 1846 AN: 4818

European-Finnish (FIN) AF: 0.402 AC: 4232 AN: 10526

Middle Eastern (MID) AF: 0.346 AC: 101 AN: 292

European-Non Finnish (NFE) AF: 0.366 AC: 24877 AN: 67946

Other (OTH) AF: 0.325 AC: 686 AN: 2110

Alfa AF: 0.353 Hom.: 30621

Bravo AF: 0.338

Asia WGS AF: 0.273 AC: 952 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	6.5
DANN	Benign	0.70
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;