chr6-79855119-C-T

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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000403623.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000220918	ENST00000403623.1	TSL:6	n.436C>T		non_coding_transcript_exon	Exon 1 of 1
	LINC01621	ENST00000784459.1		n.386+23045G>A		intron	N/A
	LINC01621	ENST00000784460.1		n.700+10339G>A		intron	N/A

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 v4.9

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;