rs1321847

chr6-79823470-A-Gchr6-79823470-A-T

Variant summary

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

The ENST00000438797.3(LINC01621):n.233+9685T>C 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 0.899 in 152,192 control chromosomes in the GnomAD database, including 61,638 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 0.90 (61638 hom., cov: 31)
• Consequence: LINC01621 ENST00000438797.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.16

Genes affected

LINC01621 (HGNC:14109): (long intergenic non-protein coding RNA 1621)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.66).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.94 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC01621	ENST00000438797.3	n.233+9685T>C		intron_variant, non_coding_transcript_variant		5
LINC01621	ENST00000669965.1	n.232+9685T>C		intron_variant, non_coding_transcript_variant
LINC01621	ENST00000693479.1	n.373+6193T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.900 AC: 136793 AN: 152074 Hom.: 61612 Cov.: 31

Gnomad AFR AF: 0.871

Gnomad AMI AF: 0.980

Gnomad AMR AF: 0.928

Gnomad ASJ AF: 0.926

Gnomad EAS AF: 0.842

Gnomad SAS AF: 0.964

Gnomad FIN AF: 0.874

Gnomad MID AF: 0.886

Gnomad NFE AF: 0.912

Gnomad OTH AF: 0.894

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

GnomAD4 genome AF: 0.899 AC: 136871 AN: 152192 Hom.: 61638 Cov.: 31 AF XY: 0.899 AC XY: 66911 AN XY: 74422

Gnomad4 AFR AF: 0.870

Gnomad4 AMR AF: 0.928

Gnomad4 ASJ AF: 0.926

Gnomad4 EAS AF: 0.841

Gnomad4 SAS AF: 0.963

Gnomad4 FIN AF: 0.874

Gnomad4 NFE AF: 0.912

Gnomad4 OTH AF: 0.892

Alfa AF: 0.911 Hom.: 120836

Bravo AF: 0.899

Asia WGS AF: 0.899 AC: 3127 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.66
Cadd	Benign	14
Dann	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1321847; hg19: chr6-80533187;