ENST00000500358.6:n.3790-12831C>G

Variant names:

• chr4-99273964-C-G
• rs1618572
• ENST00000500358.6:n.3790-12831C>G

Variant summary

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

The ENST00000500358.6(ENSG00000246090):​n.3790-12831C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.816 in 152,268 control chromosomes in the GnomAD database, including 51,057 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 0.82 (51057 hom., cov: 33)
• Consequence: ENSG00000246090 ENST00000500358.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.87
• Publications: 4 publications found

Genes affected

ENSG00000246090 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.902 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000500358.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LOC100507053	NR_037884.1		n.3790-12831C>G		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000246090	ENST00000500358.6	TSL:1	n.3790-12831C>G		intron	N/A
	ENSG00000246090	ENST00000509295.5	TSL:1	n.695-161C>G		intron	N/A
	ENSG00000246090	ENST00000506160.1	TSL:4	n.408-4489C>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.816 AC: 124169 AN: 152150 Hom.: 51004 Cov.: 33

Gnomad AFR AF: 0.910

Gnomad AMI AF: 0.813

Gnomad AMR AF: 0.805

Gnomad ASJ AF: 0.844

Gnomad EAS AF: 0.911

Gnomad SAS AF: 0.699

Gnomad FIN AF: 0.731

Gnomad MID AF: 0.766

Gnomad NFE AF: 0.774

Gnomad OTH AF: 0.825

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

GnomAD4 genome AF: 0.816 AC: 124277 AN: 152268 Hom.: 51057 Cov.: 33 AF XY: 0.811 AC XY: 60390 AN XY: 74442

African (AFR) AF: 0.910 AC: 37814 AN: 41556

American (AMR) AF: 0.805 AC: 12318 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.844 AC: 2929 AN: 3470

East Asian (EAS) AF: 0.911 AC: 4724 AN: 5188

South Asian (SAS) AF: 0.700 AC: 3378 AN: 4826

European-Finnish (FIN) AF: 0.731 AC: 7746 AN: 10592

Middle Eastern (MID) AF: 0.765 AC: 225 AN: 294

European-Non Finnish (NFE) AF: 0.774 AC: 52667 AN: 68018

Other (OTH) AF: 0.821 AC: 1735 AN: 2112

Alfa AF: 0.791 Hom.: 5573

Bravo AF: 0.830

Asia WGS AF: 0.748 AC: 2599 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.043
DANN	Benign	0.57
PhyloP100		-1.9

Splicing

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

Other links and lift over

dbSNP: rs1618572; hg19: chr4-100195121;