rs1887263

Variant names:

• chr13-22909577-G-A
• rs1887263
• ENST00000577004.3:n.749+6141C>T

Variant summary

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

The ENST00000577004.3(LINC00621):​n.749+6141C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.217 in 151,476 control chromosomes in the GnomAD database, including 3,939 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 0.22 (3939 hom., cov: 29)
• Consequence: LINC00621 ENST00000577004.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.256
• Publications: 6 publications found

Genes affected

LINC00621 (HGNC:44227): (long intergenic non-protein coding RNA 621)

ENSG00000262198 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.3 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC00621	NR_138043.1	n.652+6141C>T		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC00621	ENST00000577004.3	n.749+6141C>T		intron_variant	Intron 1 of 4	4
LINC00621	ENST00000658532.1	n.229+6141C>T		intron_variant	Intron 1 of 3
LINC00621	ENST00000663150.1	n.50+6141C>T		intron_variant	Intron 1 of 4

Frequencies

GnomAD3 genomes AF: 0.217 AC: 32852 AN: 151364 Hom.: 3919 Cov.: 29

Gnomad AFR AF: 0.304

Gnomad AMI AF: 0.247

Gnomad AMR AF: 0.246

Gnomad ASJ AF: 0.160

Gnomad EAS AF: 0.210

Gnomad SAS AF: 0.130

Gnomad FIN AF: 0.170

Gnomad MID AF: 0.239

Gnomad NFE AF: 0.175

Gnomad OTH AF: 0.209

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

GnomAD4 genome AF: 0.217 AC: 32916 AN: 151476 Hom.: 3939 Cov.: 29 AF XY: 0.217 AC XY: 16030 AN XY: 74038

African (AFR) AF: 0.304 AC: 12548 AN: 41242

American (AMR) AF: 0.247 AC: 3762 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.160 AC: 553 AN: 3466

East Asian (EAS) AF: 0.210 AC: 1077 AN: 5118

South Asian (SAS) AF: 0.130 AC: 619 AN: 4778

European-Finnish (FIN) AF: 0.170 AC: 1772 AN: 10446

Middle Eastern (MID) AF: 0.240 AC: 70 AN: 292

European-Non Finnish (NFE) AF: 0.175 AC: 11854 AN: 67870

Other (OTH) AF: 0.208 AC: 437 AN: 2102

Alfa AF: 0.188 Hom.: 12183

Bravo AF: 0.229

Asia WGS AF: 0.176 AC: 611 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	2.1
DANN	Benign	0.66
PhyloP100		-0.26

Splicing

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

Other links and lift over

dbSNP: rs1887263; hg19: chr13-23483716;