rs4770336

Positions:

• chr13-22906128-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_138043.1(LINC00621):​n.652+9590G>A variant causes a intron, non coding transcript 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 NR_138043.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.117

Genes affected

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

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
LINC00621	NR_138043.1	n.652+9590G>A		intron_variant, non_coding_transcript_variant
LOC105370109	XR_001749785.2	n.262+2566C>T		intron_variant, non_coding_transcript_variant
LOC105370109	XR_941738.1	n.300+2566C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC00621	ENST00000668623.1	n.58+9590G>A		intron_variant, non_coding_transcript_variant
	ENST00000686188.1	n.286+2566C>T		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.217

Gnomad4 AMR AF: 0.525

Gnomad4 ASJ AF: 0.628

Gnomad4 EAS AF: 0.488

Gnomad4 SAS AF: 0.623

Gnomad4 FIN AF: 0.699

Gnomad4 NFE AF: 0.659

Gnomad4 OTH AF: 0.536

Alfa AF: 0.579 Hom.: 3435

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4770336; hg19: chr13-23480267;