rs1346655

Positions:

• chr20-22413674-C-T

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

ENSG00000204684 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC284788	NR_027089.2	n.684+6286G>A		intron_variant
LOC284788	NR_027090.1	n.684+6286G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000204684	ENST00000377121.1	n.684+6286G>A		intron_variant		1
ENSG00000204684	ENST00000634280.1	n.270-6962G>A		intron_variant		5
ENSG00000204684	ENST00000635130.1	n.688+6286G>A		intron_variant		5

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

Gnomad4 AFR AF: 0.0137

Gnomad4 AMR AF: 0.108

Gnomad4 ASJ AF: 0.0593

Gnomad4 EAS AF: 0.402

Gnomad4 SAS AF: 0.0381

Gnomad4 FIN AF: 0.0638

Gnomad4 NFE AF: 0.0711

Gnomad4 OTH AF: 0.0714

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 v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1346655; hg19: chr20-22394312;