rs971206

Positions:

• chr13-22909191-G-C

Variant summary

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

The NR_138043.1(LINC00621):​n.652+6527C>G 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 0.806 in 152,100 control chromosomes in the GnomAD database, including 50,255 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 0.81 (50255 hom., cov: 31)
• Consequence: LINC00621 NR_138043.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.817

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=-1.03).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.865 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC00621	NR_138043.1	n.652+6527C>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC00621	ENST00000668623.1	n.58+6527C>G		intron_variant, non_coding_transcript_variant
	ENST00000686188.1	n.286+5629G>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.806 AC: 122452 AN: 151982 Hom.: 50235 Cov.: 31

Gnomad AFR AF: 0.631

Gnomad AMI AF: 0.828

Gnomad AMR AF: 0.862

Gnomad ASJ AF: 0.825

Gnomad EAS AF: 0.861

Gnomad SAS AF: 0.855

Gnomad FIN AF: 0.930

Gnomad MID AF: 0.771

Gnomad NFE AF: 0.871

Gnomad OTH AF: 0.811

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

GnomAD4 genome AF: 0.806 AC: 122521 AN: 152100 Hom.: 50255 Cov.: 31 AF XY: 0.811 AC XY: 60295 AN XY: 74382

Gnomad4 AFR AF: 0.631

Gnomad4 AMR AF: 0.863

Gnomad4 ASJ AF: 0.825

Gnomad4 EAS AF: 0.862

Gnomad4 SAS AF: 0.855

Gnomad4 FIN AF: 0.930

Gnomad4 NFE AF: 0.871

Gnomad4 OTH AF: 0.808

Alfa AF: 0.831 Hom.: 6596

Bravo AF: 0.793

Asia WGS AF: 0.845 AC: 2937 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.55
DANN	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs971206; hg19: chr13-23483330;