5-40502830-A-G

Variant names:

• chr5-40502830-A-G
• rs1553575
• ENST00000649444.1:n.243-1041A>G

Variant summary

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

The ENST00000649444.1(ENSG00000285552):​n.243-1041A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.643 in 152,016 control chromosomes in the GnomAD database, including 31,564 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 0.64 (31564 hom., cov: 32)
• Consequence: ENSG00000285552 ENST00000649444.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.139
• Publications: 7 publications found

Genes affected

ENSG00000285552 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.672 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000649444.1. 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
	ENSG00000285552	ENST00000649444.1		n.243-1041A>G		intron	N/A
	ENSG00000285552	ENST00000649894.1		n.120-1041A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.642 AC: 97590 AN: 151898 Hom.: 31525 Cov.: 32

Gnomad AFR AF: 0.619

Gnomad AMI AF: 0.855

Gnomad AMR AF: 0.618

Gnomad ASJ AF: 0.656

Gnomad EAS AF: 0.532

Gnomad SAS AF: 0.598

Gnomad FIN AF: 0.601

Gnomad MID AF: 0.592

Gnomad NFE AF: 0.677

Gnomad OTH AF: 0.641

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

GnomAD4 genome AF: 0.643 AC: 97680 AN: 152016 Hom.: 31564 Cov.: 32 AF XY: 0.638 AC XY: 47432 AN XY: 74296

African (AFR) AF: 0.619 AC: 25680 AN: 41458

American (AMR) AF: 0.618 AC: 9432 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.656 AC: 2276 AN: 3472

East Asian (EAS) AF: 0.532 AC: 2750 AN: 5170

South Asian (SAS) AF: 0.599 AC: 2889 AN: 4826

European-Finnish (FIN) AF: 0.601 AC: 6344 AN: 10562

Middle Eastern (MID) AF: 0.599 AC: 176 AN: 294

European-Non Finnish (NFE) AF: 0.677 AC: 45992 AN: 67954

Other (OTH) AF: 0.644 AC: 1361 AN: 2112

Alfa AF: 0.474 Hom.: 1052

Bravo AF: 0.646

Asia WGS AF: 0.594 AC: 2066 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.34
DANN	Benign	0.36
PhyloP100		0.14

Splicing

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

Other links and lift over

dbSNP: rs1553575; hg19: chr5-40502932;