8-101318165-A-G

Variant names:

• chr8-101318165-A-G
• rs10505007
• XM_047422525.1:c.217+4A>G

Variant summary

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

The ENST00000750987.1(ENSG00000297795):​n.439+4A>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 0.346 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 ENST00000750987.1 splice_region, intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.357
• Publications: 6 publications found

Genes affected

LOC124901993 (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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000750987.1. 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
	ENSG00000297795	ENST00000750988.1		n.677A>G		splice_region non_coding_transcript_exon	Exon 5 of 7
	ENSG00000297795	ENST00000750987.1		n.439+4A>G		splice_region intron	N/A
	ENSG00000297795	ENST00000750989.1		n.279+4A>G		splice_region intron	N/A

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 v4.9

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;