2-19494439-C-T

Variant names:

• chr2-19494439-C-T
• rs6705213
• ENST00000641680.1:n.530+5950C>T

Variant summary

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

The ENST00000641680.1(LINC01808):​n.530+5950C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.51 in 151,946 control chromosomes in the GnomAD database, including 20,303 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 0.51 (20303 hom., cov: 32)
• Consequence: LINC01808 ENST00000641680.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.461
• Publications: 1 publications found

Genes affected

LINC01808 (HGNC:52611): (long intergenic non-protein coding RNA 1808)

ENSG00000306962 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.552 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01808	NR_183418.1	n.605+5950C>T		intron_variant	Intron 5 of 5
LINC01808	NR_183420.1	n.544+5950C>T		intron_variant	Intron 5 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01808	ENST00000641680.1	n.530+5950C>T		intron_variant	Intron 5 of 5
LINC01808	ENST00000641932.1	n.1194+5950C>T		intron_variant	Intron 6 of 6
LINC01808	ENST00000657829.1	n.649+5950C>T		intron_variant	Intron 5 of 5

Frequencies

GnomAD3 genomes AF: 0.510 AC: 77394 AN: 151828 Hom.: 20279 Cov.: 32

Gnomad AFR AF: 0.557

Gnomad AMI AF: 0.515

Gnomad AMR AF: 0.532

Gnomad ASJ AF: 0.493

Gnomad EAS AF: 0.134

Gnomad SAS AF: 0.350

Gnomad FIN AF: 0.581

Gnomad MID AF: 0.415

Gnomad NFE AF: 0.507

Gnomad OTH AF: 0.471

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

GnomAD4 genome AF: 0.510 AC: 77465 AN: 151946 Hom.: 20303 Cov.: 32 AF XY: 0.509 AC XY: 37806 AN XY: 74266

African (AFR) AF: 0.558 AC: 23109 AN: 41434

American (AMR) AF: 0.532 AC: 8128 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.493 AC: 1712 AN: 3470

East Asian (EAS) AF: 0.134 AC: 688 AN: 5150

South Asian (SAS) AF: 0.348 AC: 1676 AN: 4818

European-Finnish (FIN) AF: 0.581 AC: 6137 AN: 10558

Middle Eastern (MID) AF: 0.408 AC: 120 AN: 294

European-Non Finnish (NFE) AF: 0.507 AC: 34442 AN: 67926

Other (OTH) AF: 0.466 AC: 984 AN: 2112

Alfa AF: 0.497 Hom.: 79453

Bravo AF: 0.505

Asia WGS AF: 0.271 AC: 949 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.19
DANN	Benign	0.40
PhyloP100		-0.46

Splicing

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

Other links and lift over

dbSNP: rs6705213; hg19: chr2-19694200;