ENST00000729586.1:n.243+2337G>A

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC112268029	XR_002956713.2	n.*45C>T		downstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC00967	ENST00000729586.1	n.243+2337G>A		intron_variant	Intron 1 of 3
LINC00967	ENST00000729587.1	n.209+1530G>A		intron_variant	Intron 1 of 3
LINC00967	ENST00000729588.1	n.175+1530G>A		intron_variant	Intron 1 of 4

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 v4.3

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

Other links and lift over

dbSNP: rs6999780; hg19: chr8-67092076;