rs10958357

Variant names:

• chr8-53407913-C-T
• rs10958357
• ENST00000521558.2:n.363-11847G>A

Variant summary

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

The ENST00000521558.2(LINC02984):​n.363-11847G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.535 in 152,114 control chromosomes in the GnomAD database, including 23,816 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 0.53 (23816 hom., cov: 32)
• Consequence: LINC02984 ENST00000521558.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.784
• Publications: 3 publications found

Genes affected

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

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.649 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02984	ENST00000521558.2	n.363-11847G>A		intron_variant	Intron 3 of 4	3
LINC02984	ENST00000653042.1	n.534-6344G>A		intron_variant	Intron 4 of 6
LINC02984	ENST00000653150.3	n.508-6344G>A		intron_variant	Intron 2 of 4

Frequencies

GnomAD3 genomes AF: 0.535 AC: 81287 AN: 151996 Hom.: 23810 Cov.: 32

Gnomad AFR AF: 0.270

Gnomad AMI AF: 0.657

Gnomad AMR AF: 0.585

Gnomad ASJ AF: 0.616

Gnomad EAS AF: 0.666

Gnomad SAS AF: 0.633

Gnomad FIN AF: 0.577

Gnomad MID AF: 0.614

Gnomad NFE AF: 0.654

Gnomad OTH AF: 0.572

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

GnomAD4 genome AF: 0.535 AC: 81328 AN: 152114 Hom.: 23816 Cov.: 32 AF XY: 0.537 AC XY: 39969 AN XY: 74374

African (AFR) AF: 0.270 AC: 11207 AN: 41486

American (AMR) AF: 0.585 AC: 8946 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.616 AC: 2135 AN: 3468

East Asian (EAS) AF: 0.666 AC: 3447 AN: 5176

South Asian (SAS) AF: 0.633 AC: 3050 AN: 4816

European-Finnish (FIN) AF: 0.577 AC: 6103 AN: 10572

Middle Eastern (MID) AF: 0.616 AC: 181 AN: 294

European-Non Finnish (NFE) AF: 0.654 AC: 44460 AN: 67988

Other (OTH) AF: 0.569 AC: 1202 AN: 2112

Alfa AF: 0.619 Hom.: 132037

Bravo AF: 0.522

Asia WGS AF: 0.633 AC: 2197 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.35
DANN	Benign	0.38
PhyloP100		-0.78

Splicing

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

Other links and lift over

dbSNP: rs10958357; hg19: chr8-54320473;