rs9341799

Variant names:

• chr6-79854802-T-C
• rs9341799
• ENST00000403623.1:n.119T>C

Your query was ambiguous. Multiple possible variants found:

• chr6-79854802-T-C
• chr6-79854802-T-G

Variant summary

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

The ENST00000403623.1(ENSG00000220918):​n.119T>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 0.361 in 151,894 control chromosomes in the GnomAD database, including 10,639 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 0.36 (10638 hom., cov: 32)
  • Exomes 𝑓: 0.30 (1 hom.)
• Consequence: ENSG00000220918 ENST00000403623.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0990
• Publications: 3 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=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.582 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

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

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000220918	ENST00000403623.1	TSL:6	n.119T>C		non_coding_transcript_exon	Exon 1 of 1
	LINC01621	ENST00000784459.1		n.386+23362A>G		intron	N/A
	LINC01621	ENST00000784460.1		n.700+10656A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.361 AC: 54841 AN: 151756 Hom.: 10627 Cov.: 32

Gnomad AFR AF: 0.246

Gnomad AMI AF: 0.476

Gnomad AMR AF: 0.458

Gnomad ASJ AF: 0.400

Gnomad EAS AF: 0.600

Gnomad SAS AF: 0.354

Gnomad FIN AF: 0.362

Gnomad MID AF: 0.484

Gnomad NFE AF: 0.388

Gnomad OTH AF: 0.384

GnomAD4 exome AF: 0.300 AC: 6 AN: 20 Hom.: 1 Cov.: 0 AF XY: 0.250 AC XY: 4 AN XY: 16

African (AFR) AF: 0.00 AC: 0 AN: 2

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.333 AC: 6 AN: 18

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.361 AC: 54892 AN: 151874 Hom.: 10638 Cov.: 32 AF XY: 0.362 AC XY: 26853 AN XY: 74196

African (AFR) AF: 0.246 AC: 10200 AN: 41478

American (AMR) AF: 0.459 AC: 7004 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.400 AC: 1386 AN: 3466

East Asian (EAS) AF: 0.600 AC: 3075 AN: 5124

South Asian (SAS) AF: 0.354 AC: 1707 AN: 4816

European-Finnish (FIN) AF: 0.362 AC: 3791 AN: 10484

Middle Eastern (MID) AF: 0.463 AC: 136 AN: 294

European-Non Finnish (NFE) AF: 0.388 AC: 26346 AN: 67922

Other (OTH) AF: 0.386 AC: 815 AN: 2112

Alfa AF: 0.384 Hom.: 41850

Bravo AF: 0.368

Asia WGS AF: 0.484 AC: 1685 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.3
DANN	Benign	0.53
PhyloP100		0.099

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs9341799;

hg19: chr6-80564519;