rs16919143

Variant names:

• chr8-53418126-C-A
• rs16919143
• ENST00000521558.2:n.362+2940G>T

Your query was ambiguous. Multiple possible variants found:

• chr8-53418126-C-A
• chr8-53418126-C-G

Variant summary

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

The ENST00000521558.2(LINC02984):​n.362+2940G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.123 in 152,202 control chromosomes in the GnomAD database, including 1,399 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 0.12 (1399 hom., cov: 32)
• Consequence: LINC02984 ENST00000521558.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.44
• 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=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.193 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.362+2940G>T		intron_variant	Intron 3 of 4	3
LINC02984	ENST00000653042.1	n.533+2940G>T		intron_variant	Intron 4 of 6
LINC02984	ENST00000653150.3	n.507+2940G>T		intron_variant	Intron 2 of 4

Frequencies

GnomAD3 genomes AF: 0.123 AC: 18665 AN: 152084 Hom.: 1396 Cov.: 32

Gnomad AFR AF: 0.197

Gnomad AMI AF: 0.0768

Gnomad AMR AF: 0.0985

Gnomad ASJ AF: 0.211

Gnomad EAS AF: 0.0782

Gnomad SAS AF: 0.112

Gnomad FIN AF: 0.0534

Gnomad MID AF: 0.152

Gnomad NFE AF: 0.0941

Gnomad OTH AF: 0.126

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

GnomAD4 genome AF: 0.123 AC: 18681 AN: 152202 Hom.: 1399 Cov.: 32 AF XY: 0.120 AC XY: 8957 AN XY: 74410

African (AFR) AF: 0.197 AC: 8155 AN: 41488

American (AMR) AF: 0.0984 AC: 1504 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.211 AC: 731 AN: 3468

East Asian (EAS) AF: 0.0783 AC: 406 AN: 5182

South Asian (SAS) AF: 0.111 AC: 535 AN: 4828

European-Finnish (FIN) AF: 0.0534 AC: 567 AN: 10610

Middle Eastern (MID) AF: 0.153 AC: 45 AN: 294

European-Non Finnish (NFE) AF: 0.0941 AC: 6403 AN: 68012

Other (OTH) AF: 0.125 AC: 265 AN: 2116

Alfa AF: 0.106 Hom.: 3254

Bravo AF: 0.128

Asia WGS AF: 0.109 AC: 378 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	0.58
DANN	Benign	0.43
PhyloP100		-2.4

Splicing

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

Other links and lift over

dbSNP: rs16919143; hg19: chr8-54330686;