rs10098823

Variant names:

• chr8-66183392-C-A
• rs10098823
• ENST00000729586.1:n.243+5888C>A

Variant summary

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

The ENST00000729586.1(LINC00967):​n.243+5888C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.156 in 152,036 control chromosomes in the GnomAD database, including 4,094 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 0.16 (4094 hom., cov: 32)
• Consequence: LINC00967 ENST00000729586.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0540
• Publications: 6 publications found

Genes affected

LINC00967 (HGNC:48725): (long intergenic non-protein coding RNA 967)

ENSG00000295392 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.426 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000729586.1. 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
	LINC00967	ENST00000729586.1		n.243+5888C>A		intron	N/A
	LINC00967	ENST00000729587.1		n.209+5081C>A		intron	N/A
	LINC00967	ENST00000729588.1		n.175+5081C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.156 AC: 23733 AN: 151918 Hom.: 4083 Cov.: 32

Gnomad AFR AF: 0.432

Gnomad AMI AF: 0.00658

Gnomad AMR AF: 0.0840

Gnomad ASJ AF: 0.0634

Gnomad EAS AF: 0.000192

Gnomad SAS AF: 0.0238

Gnomad FIN AF: 0.0609

Gnomad MID AF: 0.0665

Gnomad NFE AF: 0.0492

Gnomad OTH AF: 0.131

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

GnomAD4 genome AF: 0.156 AC: 23781 AN: 152036 Hom.: 4094 Cov.: 32 AF XY: 0.152 AC XY: 11280 AN XY: 74316

African (AFR) AF: 0.432 AC: 17876 AN: 41402

American (AMR) AF: 0.0838 AC: 1281 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.0634 AC: 220 AN: 3468

East Asian (EAS) AF: 0.000193 AC: 1 AN: 5186

South Asian (SAS) AF: 0.0240 AC: 116 AN: 4824

European-Finnish (FIN) AF: 0.0609 AC: 645 AN: 10596

Middle Eastern (MID) AF: 0.0714 AC: 21 AN: 294

European-Non Finnish (NFE) AF: 0.0492 AC: 3343 AN: 67970

Other (OTH) AF: 0.129 AC: 272 AN: 2104

Alfa AF: 0.0884 Hom.: 1097

Bravo AF: 0.168

Asia WGS AF: 0.0340 AC: 118 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.8
DANN	Benign	0.54
PhyloP100		-0.054

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs10098823;

hg19: chr8-67095627;