rs584747

Variant names:

• chr6-49799877-A-G
• rs584747
• ENST00000653295.1:n.340-17514A>G

Variant summary

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

The ENST00000653295.1(ENSG00000235122):​n.340-17514A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.136 in 152,234 control chromosomes in the GnomAD database, including 1,556 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 0.14 (1556 hom., cov: 33)
• Consequence: ENSG00000235122 ENST00000653295.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.19
• Publications: 2 publications found

Genes affected

ENSG00000235122 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.19 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000235122	ENST00000653295.1	n.340-17514A>G		intron_variant	Intron 3 of 5
ENSG00000235122	ENST00000654475.2	n.76+12391A>G		intron_variant	Intron 1 of 3
ENSG00000235122	ENST00000654478.1	n.62-3108A>G		intron_variant	Intron 1 of 5

Frequencies

GnomAD3 genomes AF: 0.136 AC: 20701 AN: 152116 Hom.: 1555 Cov.: 33

Gnomad AFR AF: 0.193

Gnomad AMI AF: 0.0724

Gnomad AMR AF: 0.0869

Gnomad ASJ AF: 0.117

Gnomad EAS AF: 0.172

Gnomad SAS AF: 0.132

Gnomad FIN AF: 0.131

Gnomad MID AF: 0.0918

Gnomad NFE AF: 0.113

Gnomad OTH AF: 0.127

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

GnomAD4 genome AF: 0.136 AC: 20725 AN: 152234 Hom.: 1556 Cov.: 33 AF XY: 0.136 AC XY: 10112 AN XY: 74434

African (AFR) AF: 0.193 AC: 8020 AN: 41540

American (AMR) AF: 0.0867 AC: 1326 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.117 AC: 406 AN: 3472

East Asian (EAS) AF: 0.172 AC: 891 AN: 5180

South Asian (SAS) AF: 0.132 AC: 635 AN: 4824

European-Finnish (FIN) AF: 0.131 AC: 1392 AN: 10600

Middle Eastern (MID) AF: 0.0918 AC: 27 AN: 294

European-Non Finnish (NFE) AF: 0.113 AC: 7694 AN: 68010

Other (OTH) AF: 0.127 AC: 268 AN: 2114

Alfa AF: 0.136 Hom.: 180

Bravo AF: 0.136

Asia WGS AF: 0.151 AC: 526 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.1
DANN	Benign	0.65
PhyloP100		1.2

Splicing

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

Other links and lift over

dbSNP: rs584747; hg19: chr6-49767590;