8-76504958-G-T

Variant names:

• chr8-76504958-G-T
• rs16939284
• ENST00000518732.1:n.333-5433G>T

Variant summary

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

The ENST00000518732.1(LINC01111):​n.333-5433G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.187 in 151,960 control chromosomes in the GnomAD database, including 3,579 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 0.19 (3579 hom., cov: 32)
• Consequence: LINC01111 ENST00000518732.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.20
• Publications: 1 publications found

Genes affected

LINC01111 (HGNC:49237): (long intergenic non-protein coding RNA 1111)

ZFHX4-AS1 (HGNC:44165): (ZFHX4 antisense RNA 1)

LOC107986952 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.356 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000518732.1. 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
	LINC01111	NR_105006.1		n.333-5433G>T		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01111	ENST00000518732.1	TSL:1	n.333-5433G>T		intron	N/A
	ZFHX4-AS1	ENST00000522961.2	TSL:5	n.231-2112C>A		intron	N/A
	ZFHX4-AS1	ENST00000814135.1		n.346-13727C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.187 AC: 28374 AN: 151842 Hom.: 3569 Cov.: 32

Gnomad AFR AF: 0.360

Gnomad AMI AF: 0.0943

Gnomad AMR AF: 0.139

Gnomad ASJ AF: 0.207

Gnomad EAS AF: 0.0607

Gnomad SAS AF: 0.139

Gnomad FIN AF: 0.0994

Gnomad MID AF: 0.225

Gnomad NFE AF: 0.119

Gnomad OTH AF: 0.186

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

GnomAD4 genome AF: 0.187 AC: 28424 AN: 151960 Hom.: 3579 Cov.: 32 AF XY: 0.185 AC XY: 13754 AN XY: 74268

African (AFR) AF: 0.360 AC: 14926 AN: 41406

American (AMR) AF: 0.139 AC: 2120 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.207 AC: 718 AN: 3472

East Asian (EAS) AF: 0.0609 AC: 313 AN: 5142

South Asian (SAS) AF: 0.139 AC: 669 AN: 4804

European-Finnish (FIN) AF: 0.0994 AC: 1052 AN: 10586

Middle Eastern (MID) AF: 0.224 AC: 66 AN: 294

European-Non Finnish (NFE) AF: 0.119 AC: 8079 AN: 67980

Other (OTH) AF: 0.187 AC: 395 AN: 2108

Alfa AF: 0.134 Hom.: 2803

Bravo AF: 0.197

Asia WGS AF: 0.126 AC: 439 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.096
DANN	Benign	0.43
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs16939284; hg19: chr8-77417193;