8-66178947-G-T

Variant names:

• chr8-66178947-G-T
• rs12721510
• ENST00000729586.1:n.243+1443G>T

Variant summary

Our verdict is Benign. The variant received -13 ACMG points: 0P and 13B. BP4_Strong BP6 BA1

The ENST00000729586.1(LINC00967):​n.243+1443G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0419 in 152,228 control chromosomes in the GnomAD database, including 186 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (no stars).

• Frequency: Genomes: 𝑓 0.042 (186 hom., cov: 32)
• Consequence: LINC00967 ENST00000729586.1 intron
• Clinical Significance: Likely benign no assertion criteria provided B:1 O:1
• Conservation: PhyloP100: -0.394
• Publications: 11 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -13 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BP6: Variant 8-66178947-G-T is Benign according to our data. Variant chr8-66178947-G-T is described in ClinVar as Likely_benign. ClinVar VariationId is 38800.Status of the report is no_assertion_criteria_provided, 0 stars.
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0609 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+1443G>T		intron	N/A
	LINC00967	ENST00000729587.1		n.209+636G>T		intron	N/A
	LINC00967	ENST00000729588.1		n.175+636G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0419 AC: 6376 AN: 152110 Hom.: 186 Cov.: 32

Gnomad AFR AF: 0.0107

Gnomad AMI AF: 0.0286

Gnomad AMR AF: 0.0346

Gnomad ASJ AF: 0.0922

Gnomad EAS AF: 0.000193

Gnomad SAS AF: 0.0126

Gnomad FIN AF: 0.0601

Gnomad MID AF: 0.0601

Gnomad NFE AF: 0.0625

Gnomad OTH AF: 0.0421

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

GnomAD4 genome AF: 0.0419 AC: 6373 AN: 152228 Hom.: 186 Cov.: 32 AF XY: 0.0410 AC XY: 3054 AN XY: 74426

African (AFR) AF: 0.0107 AC: 445 AN: 41550

American (AMR) AF: 0.0346 AC: 529 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.0922 AC: 320 AN: 3472

East Asian (EAS) AF: 0.000193 AC: 1 AN: 5180

South Asian (SAS) AF: 0.0127 AC: 61 AN: 4822

European-Finnish (FIN) AF: 0.0601 AC: 637 AN: 10594

Middle Eastern (MID) AF: 0.0612 AC: 18 AN: 294

European-Non Finnish (NFE) AF: 0.0625 AC: 4248 AN: 68002

Other (OTH) AF: 0.0417 AC: 88 AN: 2112

Alfa AF: 0.0557 Hom.: 524

Bravo AF: 0.0388

Asia WGS AF: 0.00462 AC: 16 AN: 3478

ClinVar

ClinVar submissions

Significance: Likely benign

Revision: no assertion criteria provided

Pathogenic	VUS	Benign	Condition
-	-	1	CRH-related disorder (1)
-	-	-	Autosomal dominant nocturnal frontal lobe epilepsy (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	1.6
DANN	Benign	0.50
PhyloP100		-0.39
PromoterAI		0.062	Neutral

Splicing

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

Other links and lift over

dbSNP: rs12721510; hg19: chr8-67091182;