rs346291

Variant names:

• chr6-79855119-C-T
• rs346291
• ENST00000403623.1:n.436C>T

Variant summary

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

The ENST00000403623.1(ENSG00000220918):​n.436C>T 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 0.427 in 152,124 control chromosomes in the GnomAD database, including 15,864 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 0.43 (15854 hom., cov: 31)
  • Exomes 𝑓: 0.30 (10 hom.)
• Consequence: ENSG00000220918 ENST00000403623.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0600
• Publications: 10 publications found

Genes affected

ENSG00000220918 (HGNC:):

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=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.657 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC100422671		n.79855119C>T		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000220918	ENST00000403623.1	n.436C>T		non_coding_transcript_exon_variant	Exon 1 of 1	6
LINC01621	ENST00000784459.1	n.386+23045G>A		intron_variant	Intron 1 of 3
LINC01621	ENST00000784460.1	n.700+10339G>A		intron_variant	Intron 3 of 5

Frequencies

GnomAD3 genomes AF: 0.427 AC: 64780 AN: 151792 Hom.: 15837 Cov.: 31

Gnomad AFR AF: 0.664

Gnomad AMI AF: 0.199

Gnomad AMR AF: 0.292

Gnomad ASJ AF: 0.285

Gnomad EAS AF: 0.197

Gnomad SAS AF: 0.475

Gnomad FIN AF: 0.292

Gnomad MID AF: 0.310

Gnomad NFE AF: 0.359

Gnomad OTH AF: 0.382

GnomAD4 exome AF: 0.301 AC: 65 AN: 216 Hom.: 10 Cov.: 0 AF XY: 0.225 AC XY: 27 AN XY: 120

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 4

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.311 AC: 59 AN: 190

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.278 AC: 5 AN: 18

Other (OTH) AF: 0.250 AC: 1 AN: 4

GnomAD4 genome AF: 0.427 AC: 64844 AN: 151908 Hom.: 15854 Cov.: 31 AF XY: 0.423 AC XY: 31373 AN XY: 74222

African (AFR) AF: 0.664 AC: 27525 AN: 41454

American (AMR) AF: 0.292 AC: 4457 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.285 AC: 989 AN: 3470

East Asian (EAS) AF: 0.197 AC: 1013 AN: 5136

South Asian (SAS) AF: 0.475 AC: 2286 AN: 4810

European-Finnish (FIN) AF: 0.292 AC: 3077 AN: 10522

Middle Eastern (MID) AF: 0.333 AC: 98 AN: 294

European-Non Finnish (NFE) AF: 0.359 AC: 24413 AN: 67934

Other (OTH) AF: 0.381 AC: 805 AN: 2114

Alfa AF: 0.374 Hom.: 49984

Bravo AF: 0.431

Asia WGS AF: 0.347 AC: 1208 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	1.1
DANN	Benign	0.47
PhyloP100		0.060

Splicing

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

Other links and lift over

dbSNP: rs346291; hg19: chr6-80564836;