rs2021512

Variant names:

• chr16-24241601-G-A
• rs2021512
• ENST00000567127.1:n.33+5465G>A

Your query was ambiguous. Multiple possible variants found:

• chr16-24241601-G-A
• chr16-24241601-G-C

Variant summary

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

The ENST00000567127.1(LINC02194):​n.33+5465G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.362 in 151,046 control chromosomes in the GnomAD database, including 11,584 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 0.36 (11584 hom., cov: 28)
• Consequence: LINC02194 ENST00000567127.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.05
• Publications: 2 publications found

Genes affected

LINC02194 (HGNC:53057): (long intergenic non-protein coding RNA 2194)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.592 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02194	NR_146569.1	n.33+5465G>A		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02194	ENST00000567127.1	n.33+5465G>A		intron_variant	Intron 1 of 3	3
LINC02194	ENST00000567624.1	n.52+3568G>A		intron_variant	Intron 1 of 1	3
LINC02194	ENST00000747929.1	n.236+3549G>A		intron_variant	Intron 2 of 4

Frequencies

GnomAD3 genomes AF: 0.362 AC: 54646 AN: 150930 Hom.: 11577 Cov.: 28

Gnomad AFR AF: 0.599

Gnomad AMI AF: 0.181

Gnomad AMR AF: 0.303

Gnomad ASJ AF: 0.334

Gnomad EAS AF: 0.400

Gnomad SAS AF: 0.313

Gnomad FIN AF: 0.243

Gnomad MID AF: 0.325

Gnomad NFE AF: 0.255

Gnomad OTH AF: 0.343

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

GnomAD4 genome AF: 0.362 AC: 54682 AN: 151046 Hom.: 11584 Cov.: 28 AF XY: 0.361 AC XY: 26631 AN XY: 73766

African (AFR) AF: 0.598 AC: 24611 AN: 41154

American (AMR) AF: 0.303 AC: 4608 AN: 15200

Ashkenazi Jewish (ASJ) AF: 0.334 AC: 1155 AN: 3454

East Asian (EAS) AF: 0.400 AC: 2053 AN: 5128

South Asian (SAS) AF: 0.314 AC: 1500 AN: 4784

European-Finnish (FIN) AF: 0.243 AC: 2523 AN: 10364

Middle Eastern (MID) AF: 0.322 AC: 94 AN: 292

European-Non Finnish (NFE) AF: 0.255 AC: 17262 AN: 67662

Other (OTH) AF: 0.339 AC: 711 AN: 2098

Alfa AF: 0.313 Hom.: 1046

Bravo AF: 0.376

Asia WGS AF: 0.349 AC: 1218 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.017
DANN	Benign	0.32
PhyloP100		-2.1

Splicing

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

Other links and lift over

dbSNP: rs2021512; hg19: chr16-24252922;