rs4770336

Variant names:

• chr13-22906128-C-T
• rs4770336
• ENST00000577004.3:n.749+9590G>A

Variant summary

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

The ENST00000577004.3(LINC00621):​n.749+9590G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.517 in 151,816 control chromosomes in the GnomAD database, including 23,123 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 0.52 (23123 hom., cov: 32)
• Consequence: LINC00621 ENST00000577004.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.117
• Publications: 2 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=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.654 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC00621	NR_138043.1	n.652+9590G>A		intron_variant	Intron 1 of 2
LOC105370109	NR_187640.1	n.262+2566C>T		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC00621	ENST00000577004.3	n.749+9590G>A		intron_variant	Intron 1 of 4	4
LINC00621	ENST00000658532.1	n.229+9590G>A		intron_variant	Intron 1 of 3
LINC00621	ENST00000663150.1	n.50+9590G>A		intron_variant	Intron 1 of 4

Frequencies

GnomAD3 genomes AF: 0.518 AC: 78531 AN: 151698 Hom.: 23132 Cov.: 32

Gnomad AFR AF: 0.217

Gnomad AMI AF: 0.521

Gnomad AMR AF: 0.525

Gnomad ASJ AF: 0.628

Gnomad EAS AF: 0.489

Gnomad SAS AF: 0.623

Gnomad FIN AF: 0.699

Gnomad MID AF: 0.513

Gnomad NFE AF: 0.659

Gnomad OTH AF: 0.537

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

GnomAD4 genome AF: 0.517 AC: 78520 AN: 151816 Hom.: 23123 Cov.: 32 AF XY: 0.520 AC XY: 38611 AN XY: 74192

African (AFR) AF: 0.217 AC: 8986 AN: 41436

American (AMR) AF: 0.525 AC: 8016 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.628 AC: 2175 AN: 3464

East Asian (EAS) AF: 0.488 AC: 2519 AN: 5158

South Asian (SAS) AF: 0.623 AC: 2995 AN: 4808

European-Finnish (FIN) AF: 0.699 AC: 7365 AN: 10534

Middle Eastern (MID) AF: 0.500 AC: 147 AN: 294

European-Non Finnish (NFE) AF: 0.659 AC: 44712 AN: 67830

Other (OTH) AF: 0.536 AC: 1130 AN: 2108

Alfa AF: 0.564 Hom.: 3456

Bravo AF: 0.487

Asia WGS AF: 0.555 AC: 1930 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	6.4
DANN	Benign	0.71
PhyloP100		0.12

Splicing

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

Other links and lift over

dbSNP: rs4770336; hg19: chr13-23480267;