chr8-66179144-A-G

Variant names:

• chr8-66179144-A-G
• rs3176921
• ENST00000729586.1:n.243+1640A>G

Variant summary

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

The ENST00000729586.1(LINC00967):​n.243+1640A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.234 in 152,130 control chromosomes in the GnomAD database, including 8,406 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 0.23 (8406 hom., cov: 32)
• Consequence: LINC00967 ENST00000729586.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.340
• Publications: 21 publications found

Genes affected

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=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.603 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC00967	ENST00000729586.1		n.243+1640A>G		intron	N/A
	LINC00967	ENST00000729587.1		n.209+833A>G		intron	N/A
	LINC00967	ENST00000729588.1		n.175+833A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.233 AC: 35494 AN: 152012 Hom.: 8374 Cov.: 32

Gnomad AFR AF: 0.609

Gnomad AMI AF: 0.0636

Gnomad AMR AF: 0.123

Gnomad ASJ AF: 0.0732

Gnomad EAS AF: 0.000578

Gnomad SAS AF: 0.0329

Gnomad FIN AF: 0.0961

Gnomad MID AF: 0.0981

Gnomad NFE AF: 0.0958

Gnomad OTH AF: 0.191

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

GnomAD4 genome AF: 0.234 AC: 35579 AN: 152130 Hom.: 8406 Cov.: 32 AF XY: 0.227 AC XY: 16919 AN XY: 74390

African (AFR) AF: 0.610 AC: 25260 AN: 41438

American (AMR) AF: 0.123 AC: 1883 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.0732 AC: 254 AN: 3468

East Asian (EAS) AF: 0.000579 AC: 3 AN: 5180

South Asian (SAS) AF: 0.0332 AC: 160 AN: 4826

European-Finnish (FIN) AF: 0.0961 AC: 1019 AN: 10602

Middle Eastern (MID) AF: 0.102 AC: 30 AN: 294

European-Non Finnish (NFE) AF: 0.0958 AC: 6513 AN: 68000

Other (OTH) AF: 0.189 AC: 399 AN: 2108

Alfa AF: 0.134 Hom.: 3637

Bravo AF: 0.250

Asia WGS AF: 0.0590 AC: 209 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	8.9
DANN	Benign	0.61
PhyloP100		0.34

Splicing

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

Other links and lift over

dbSNP: rs3176921; hg19: chr8-67091379;