ENST00000500358.6:n.429-12485T>C

Variant names:

• chr4-99121070-T-C
• rs6532795
• ENST00000500358.6:n.429-12485T>C

Variant summary

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

The ENST00000500358.6(ENSG00000246090):​n.429-12485T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.754 in 152,044 control chromosomes in the GnomAD database, including 43,715 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 0.75 (43715 hom., cov: 32)
• Consequence: ENSG00000246090 ENST00000500358.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.553
• Publications: 11 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=-0.77).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.975 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC100507053	NR_037884.1	n.429-12485T>C		intron_variant	Intron 1 of 9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000246090	ENST00000500358.6	n.429-12485T>C		intron_variant	Intron 1 of 9	1
ENSG00000246090	ENST00000661393.1	n.426-12485T>C		intron_variant	Intron 1 of 9
ENSG00000246090	ENST00000670724.2	n.481-12485T>C		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.754 AC: 114518 AN: 151928 Hom.: 43670 Cov.: 32

Gnomad AFR AF: 0.826

Gnomad AMI AF: 0.655

Gnomad AMR AF: 0.756

Gnomad ASJ AF: 0.675

Gnomad EAS AF: 0.998

Gnomad SAS AF: 0.864

Gnomad FIN AF: 0.719

Gnomad MID AF: 0.756

Gnomad NFE AF: 0.694

Gnomad OTH AF: 0.730

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

GnomAD4 genome AF: 0.754 AC: 114622 AN: 152044 Hom.: 43715 Cov.: 32 AF XY: 0.762 AC XY: 56622 AN XY: 74320

African (AFR) AF: 0.826 AC: 34264 AN: 41478

American (AMR) AF: 0.756 AC: 11561 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.675 AC: 2340 AN: 3468

East Asian (EAS) AF: 0.998 AC: 5163 AN: 5174

South Asian (SAS) AF: 0.865 AC: 4174 AN: 4828

European-Finnish (FIN) AF: 0.719 AC: 7591 AN: 10556

Middle Eastern (MID) AF: 0.759 AC: 223 AN: 294

European-Non Finnish (NFE) AF: 0.694 AC: 47159 AN: 67936

Other (OTH) AF: 0.733 AC: 1550 AN: 2114

Alfa AF: 0.706 Hom.: 47275

Bravo AF: 0.758

Asia WGS AF: 0.909 AC: 3161 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	7.3
DANN	Benign	0.64
PhyloP100		0.55

Splicing

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

Other links and lift over

dbSNP: rs6532795; hg19: chr4-100042221;