rs6999780

Variant names:

• chr8-66179841-G-A
• rs6999780
• ENST00000729586.1:n.243+2337G>A

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000729586.1(LINC00967):​n.243+2337G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.159 in 152,188 control chromosomes in the GnomAD database, including 3,152 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 (3152 hom., cov: 32)
• Consequence: LINC00967 ENST00000729586.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0560
• Publications: 3 publications found

Genes affected

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

LOC112268029 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.29).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.353 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+2337G>A		intron	N/A
	LINC00967	ENST00000729587.1		n.209+1530G>A		intron	N/A
	LINC00967	ENST00000729588.1		n.175+1530G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.159 AC: 24192 AN: 152070 Hom.: 3144 Cov.: 32

Gnomad AFR AF: 0.357

Gnomad AMI AF: 0.0637

Gnomad AMR AF: 0.0883

Gnomad ASJ AF: 0.0522

Gnomad EAS AF: 0.000577

Gnomad SAS AF: 0.0334

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: 24241 AN: 152188 Hom.: 3152 Cov.: 32 AF XY: 0.156 AC XY: 11591 AN XY: 74398

African (AFR) AF: 0.357 AC: 14824 AN: 41474

American (AMR) AF: 0.0880 AC: 1347 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.0522 AC: 181 AN: 3470

East Asian (EAS) AF: 0.000578 AC: 3 AN: 5190

South Asian (SAS) AF: 0.0336 AC: 162 AN: 4818

European-Finnish (FIN) AF: 0.0960 AC: 1018 AN: 10602

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

European-Non Finnish (NFE) AF: 0.0935 AC: 6357 AN: 68016

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

Alfa AF: 0.108 Hom.: 1694

Bravo AF: 0.166

Asia WGS AF: 0.0450 AC: 158 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.29
CADD	Benign	14
DANN	Benign	0.68
PhyloP100		-0.056

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: rs6999780;

hg19: chr8-67092076;