chr6-79823470-A-G

Variant names:

• chr6-79823470-A-G
• rs1321847
• ENST00000784465.1:n.238T>C

Variant summary

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

The ENST00000784465.1(LINC01621):​n.238T>C variant causes a non coding transcript exon 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 ENST00000784465.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.16
• Publications: 7 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01621	ENST00000784465.1	n.238T>C		non_coding_transcript_exon_variant	Exon 2 of 6
LINC01621	ENST00000784467.1	n.242T>C		non_coding_transcript_exon_variant	Exon 2 of 5
LINC01621	ENST00000784473.1	n.397T>C		non_coding_transcript_exon_variant	Exon 3 of 7

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

African (AFR) AF: 0.870 AC: 36128 AN: 41512

American (AMR) AF: 0.928 AC: 14201 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.926 AC: 3212 AN: 3468

East Asian (EAS) AF: 0.841 AC: 4350 AN: 5170

South Asian (SAS) AF: 0.963 AC: 4645 AN: 4822

European-Finnish (FIN) AF: 0.874 AC: 9269 AN: 10608

Middle Eastern (MID) AF: 0.888 AC: 261 AN: 294

European-Non Finnish (NFE) AF: 0.912 AC: 62029 AN: 68000

Other (OTH) AF: 0.892 AC: 1884 AN: 2112

Alfa AF: 0.909 Hom.: 262100

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
PhyloP100		1.2

Splicing

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

Other links and lift over

dbSNP: rs1321847; hg19: chr6-80533187;