rs1346655

Variant names:

• chr20-22413674-C-T
• rs1346655
• ENST00000377121.1:n.684+6286G>A

Variant summary

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

The ENST00000377121.1(ENSG00000204684):​n.684+6286G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0686 in 152,256 control chromosomes in the GnomAD database, including 754 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 0.069 (754 hom., cov: 32)
• Consequence: ENSG00000204684 ENST00000377121.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.586
• Publications: 0 publications found

Genes affected

ENSG00000204684 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.387 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000377121.1. 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
	LOC284788	NR_027089.2		n.684+6286G>A		intron	N/A
	LOC284788	NR_027090.1		n.684+6286G>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000204684	ENST00000377121.1	TSL:1	n.684+6286G>A		intron	N/A
	ENSG00000204684	ENST00000634280.1	TSL:5	n.270-6962G>A		intron	N/A
	ENSG00000204684	ENST00000635130.1	TSL:5	n.688+6286G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0686 AC: 10440 AN: 152138 Hom.: 751 Cov.: 32

Gnomad AFR AF: 0.0138

Gnomad AMI AF: 0.0724

Gnomad AMR AF: 0.108

Gnomad ASJ AF: 0.0593

Gnomad EAS AF: 0.401

Gnomad SAS AF: 0.0381

Gnomad FIN AF: 0.0638

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.0711

Gnomad OTH AF: 0.0707

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

GnomAD4 genome AF: 0.0686 AC: 10446 AN: 152256 Hom.: 754 Cov.: 32 AF XY: 0.0703 AC XY: 5235 AN XY: 74438

African (AFR) AF: 0.0137 AC: 570 AN: 41556

American (AMR) AF: 0.108 AC: 1651 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0593 AC: 206 AN: 3472

East Asian (EAS) AF: 0.402 AC: 2077 AN: 5170

South Asian (SAS) AF: 0.0381 AC: 184 AN: 4824

European-Finnish (FIN) AF: 0.0638 AC: 676 AN: 10596

Middle Eastern (MID) AF: 0.105 AC: 31 AN: 294

European-Non Finnish (NFE) AF: 0.0711 AC: 4834 AN: 68022

Other (OTH) AF: 0.0714 AC: 151 AN: 2114

Alfa AF: 0.0775 Hom.: 87

Bravo AF: 0.0744

Asia WGS AF: 0.154 AC: 533 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	4.4
DANN	Benign	0.45
PhyloP100		0.59

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: rs1346655;

hg19: chr20-22394312;