8-76504958-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_105006.1(LINC01111):n.333-5433G>T variant causes a intron, non coding transcript 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 NR_105006.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.20

Genes affected

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

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

LOC107986952 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC01111	NR_105006.1	n.333-5433G>T		intron_variant, non_coding_transcript_variant
LOC107986952	XR_001745962.2	n.346-2112C>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC01111	ENST00000518732.1	n.333-5433G>T		intron_variant, non_coding_transcript_variant		1
ZFHX4-AS1	ENST00000522961.1	n.106-2112C>A		intron_variant, non_coding_transcript_variant		5

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

Gnomad4 AFR AF: 0.360

Gnomad4 AMR AF: 0.139

Gnomad4 ASJ AF: 0.207

Gnomad4 EAS AF: 0.0609

Gnomad4 SAS AF: 0.139

Gnomad4 FIN AF: 0.0994

Gnomad4 NFE AF: 0.119

Gnomad4 OTH AF: 0.187

Alfa AF: 0.125 Hom.: 1802

Bravo AF: 0.197

Asia WGS AF: 0.126 AC: 439 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.096
Dann	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs16939284; hg19: chr8-77417193;