rs6472258

Variant names:

• chr8-66184244-A-C
• rs6472258
• ENST00000729586.1:n.243+6740A>C

Variant summary

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

The ENST00000729586.1(LINC00967):​n.243+6740A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.101 in 148,764 control chromosomes in the GnomAD database, including 1,215 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 0.10 (1215 hom., cov: 32)
• Consequence: LINC00967 ENST00000729586.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.599
• Publications: 1 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=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.328 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+6740A>C		intron	N/A
	LINC00967	ENST00000729587.1		n.209+5933A>C		intron	N/A
	LINC00967	ENST00000729588.1		n.176-4588A>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.100 AC: 14938 AN: 148654 Hom.: 1209 Cov.: 32

Gnomad AFR AF: 0.0901

Gnomad AMI AF: 0.0143

Gnomad AMR AF: 0.241

Gnomad ASJ AF: 0.0490

Gnomad EAS AF: 0.342

Gnomad SAS AF: 0.153

Gnomad FIN AF: 0.0547

Gnomad MID AF: 0.0538

Gnomad NFE AF: 0.0642

Gnomad OTH AF: 0.0939

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

GnomAD4 genome AF: 0.101 AC: 14959 AN: 148764 Hom.: 1215 Cov.: 32 AF XY: 0.105 AC XY: 7632 AN XY: 72850

African (AFR) AF: 0.0900 AC: 3441 AN: 38220

American (AMR) AF: 0.241 AC: 3657 AN: 15166

Ashkenazi Jewish (ASJ) AF: 0.0490 AC: 170 AN: 3468

East Asian (EAS) AF: 0.342 AC: 1770 AN: 5180

South Asian (SAS) AF: 0.152 AC: 731 AN: 4822

European-Finnish (FIN) AF: 0.0547 AC: 580 AN: 10606

Middle Eastern (MID) AF: 0.0544 AC: 16 AN: 294

European-Non Finnish (NFE) AF: 0.0642 AC: 4368 AN: 68018

Other (OTH) AF: 0.103 AC: 213 AN: 2078

Alfa AF: 0.0802 Hom.: 111

Bravo AF: 0.114

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	2.0
DANN	Benign	0.70
PhyloP100		-0.60

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: rs6472258;

hg19: chr8-67096479;