8-66179945-C-T

Variant names:

• chr8-66179945-C-T
• rs6472257
• XR_002956713.2:n.264G>A

Variant summary

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

The XR_002956713.2(LOC112268029):​n.264G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.159 in 152,162 control chromosomes in the GnomAD database, including 3,149 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 (3149 hom., cov: 32)
• Consequence: LOC112268029 XR_002956713.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.187
• Publications: 9 publications found

Genes affected

LOC112268029 (HGNC:):

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

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.6).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.352 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC00967	ENST00000729586.1		n.243+2441C>T		intron	N/A
	LINC00967	ENST00000729587.1		n.209+1634C>T		intron	N/A
	LINC00967	ENST00000729588.1		n.175+1634C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.159 AC: 24177 AN: 152044 Hom.: 3141 Cov.: 32

Gnomad AFR AF: 0.357

Gnomad AMI AF: 0.0636

Gnomad AMR AF: 0.0881

Gnomad ASJ AF: 0.0524

Gnomad EAS AF: 0.000577

Gnomad SAS AF: 0.0333

Gnomad FIN AF: 0.0960

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.0935

Gnomad OTH AF: 0.129

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

GnomAD4 genome AF: 0.159 AC: 24226 AN: 152162 Hom.: 3149 Cov.: 32 AF XY: 0.156 AC XY: 11577 AN XY: 74412

African (AFR) AF: 0.357 AC: 14815 AN: 41464

American (AMR) AF: 0.0878 AC: 1344 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.0524 AC: 182 AN: 3472

East Asian (EAS) AF: 0.000578 AC: 3 AN: 5188

South Asian (SAS) AF: 0.0336 AC: 162 AN: 4826

European-Finnish (FIN) AF: 0.0960 AC: 1016 AN: 10588

Middle Eastern (MID) AF: 0.0748 AC: 22 AN: 294

European-Non Finnish (NFE) AF: 0.0935 AC: 6355 AN: 68004

Other (OTH) AF: 0.127 AC: 269 AN: 2114

Alfa AF: 0.110 Hom.: 330

Bravo AF: 0.166

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.60
CADD	Benign	16
DANN	Benign	0.67
PhyloP100		0.19

Splicing

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

Other links and lift over

dbSNP: rs6472257; hg19: chr8-67092180;