rs2838891

Variant names:

• chr21-45351569-G-A
• rs2838891
• ENST00000454115.8:n.3401-1796G>A

Variant summary

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

The ENST00000454115.8(LINC00205):​n.3401-1796G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.375 in 152,188 control chromosomes in the GnomAD database, including 11,567 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 0.38 (11567 hom., cov: 35)
• Consequence: LINC00205 ENST00000454115.8 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.799
• Publications: 5 publications found

Genes affected

LINC00205 (HGNC:16420): (long intergenic non-protein coding RNA 205)

LINC00316 (HGNC:19723): (long intergenic non-protein coding RNA 316)

LOC105372839 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.454 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105372839	XR_937800.3	n.122-1796G>A		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC00205	ENST00000454115.8	n.3401-1796G>A		intron_variant	Intron 3 of 3	1
LINC00205	ENST00000689879.3	n.168-1796G>A		intron_variant	Intron 1 of 1
LINC00205	ENST00000716679.1	n.3544-1796G>A		intron_variant	Intron 5 of 5

Frequencies

GnomAD3 genomes AF: 0.375 AC: 57060 AN: 152070 Hom.: 11566 Cov.: 35

Gnomad AFR AF: 0.250

Gnomad AMI AF: 0.442

Gnomad AMR AF: 0.340

Gnomad ASJ AF: 0.543

Gnomad EAS AF: 0.237

Gnomad SAS AF: 0.466

Gnomad FIN AF: 0.344

Gnomad MID AF: 0.487

Gnomad NFE AF: 0.458

Gnomad OTH AF: 0.394

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

GnomAD4 genome AF: 0.375 AC: 57078 AN: 152188 Hom.: 11567 Cov.: 35 AF XY: 0.373 AC XY: 27720 AN XY: 74404

African (AFR) AF: 0.250 AC: 10372 AN: 41534

American (AMR) AF: 0.340 AC: 5193 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.543 AC: 1883 AN: 3466

East Asian (EAS) AF: 0.238 AC: 1231 AN: 5174

South Asian (SAS) AF: 0.465 AC: 2247 AN: 4830

European-Finnish (FIN) AF: 0.344 AC: 3651 AN: 10598

Middle Eastern (MID) AF: 0.473 AC: 139 AN: 294

European-Non Finnish (NFE) AF: 0.458 AC: 31129 AN: 67972

Other (OTH) AF: 0.393 AC: 831 AN: 2114

Alfa AF: 0.442 Hom.: 15386

Bravo AF: 0.368

Asia WGS AF: 0.343 AC: 1190 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.2
DANN	Benign	0.72
PhyloP100		-0.80

Splicing

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

Other links and lift over

dbSNP: rs2838891; hg19: chr21-46771484;