8-53508661-A-G

Position:

• chr8-53508661-A-G

Variant summary

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

The ENST00000656976.1(LINC02984):​n.879+8051T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.788 in 152,168 control chromosomes in the GnomAD database, including 47,584 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 0.79 (47584 hom., cov: 32)
• Consequence: LINC02984 ENST00000656976.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.75

Genes affected

LINC02984 (HGNC:56063): (long intergenic non-protein coding RNA 2984)

LOC124901947 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.871 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC124901947	XR_007060913.1	n.146-16971A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC02984	ENST00000656976.1	n.879+8051T>C		intron_variant

Frequencies

GnomAD3 genomes AF: 0.788 AC: 119823 AN: 152050 Hom.: 47550 Cov.: 32

Gnomad AFR AF: 0.862

Gnomad AMI AF: 0.615

Gnomad AMR AF: 0.835

Gnomad ASJ AF: 0.775

Gnomad EAS AF: 0.893

Gnomad SAS AF: 0.812

Gnomad FIN AF: 0.677

Gnomad MID AF: 0.807

Gnomad NFE AF: 0.743

Gnomad OTH AF: 0.804

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

GnomAD4 genome AF: 0.788 AC: 119914 AN: 152168 Hom.: 47584 Cov.: 32 AF XY: 0.786 AC XY: 58503 AN XY: 74386

Gnomad4 AFR AF: 0.862

Gnomad4 AMR AF: 0.835

Gnomad4 ASJ AF: 0.775

Gnomad4 EAS AF: 0.892

Gnomad4 SAS AF: 0.813

Gnomad4 FIN AF: 0.677

Gnomad4 NFE AF: 0.743

Gnomad4 OTH AF: 0.804

Alfa AF: 0.753 Hom.: 64093

Bravo AF: 0.804

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.12
DANN	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1477958; hg19: chr8-54421221;