rs13123099

Variant names:

• chr4-99273360-G-A
• rs13123099
• ENST00000500358.6:n.3790-13435G>A

Variant summary

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

The ENST00000500358.6(ENSG00000246090):​n.3790-13435G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.275 in 152,098 control chromosomes in the GnomAD database, including 7,056 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 0.27 (7056 hom., cov: 32)
• Consequence: ENSG00000246090 ENST00000500358.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.353
• Publications: 5 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=-1.0).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.382 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC100507053	NR_037884.1	n.3790-13435G>A		intron_variant	Intron 4 of 9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000246090	ENST00000500358.6	n.3790-13435G>A		intron_variant	Intron 4 of 9	1
ENSG00000246090	ENST00000509295.5	n.695-765G>A		intron_variant	Intron 4 of 5	1
ENSG00000246090	ENST00000506160.1	n.408-5093G>A		intron_variant	Intron 3 of 4	4

Frequencies

GnomAD3 genomes AF: 0.275 AC: 41751 AN: 151980 Hom.: 7060 Cov.: 32

Gnomad AFR AF: 0.100

Gnomad AMI AF: 0.471

Gnomad AMR AF: 0.263

Gnomad ASJ AF: 0.462

Gnomad EAS AF: 0.0262

Gnomad SAS AF: 0.155

Gnomad FIN AF: 0.346

Gnomad MID AF: 0.367

Gnomad NFE AF: 0.386

Gnomad OTH AF: 0.331

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

GnomAD4 genome AF: 0.275 AC: 41752 AN: 152098 Hom.: 7056 Cov.: 32 AF XY: 0.268 AC XY: 19924 AN XY: 74354

African (AFR) AF: 0.100 AC: 4166 AN: 41528

American (AMR) AF: 0.263 AC: 4016 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.462 AC: 1602 AN: 3470

East Asian (EAS) AF: 0.0262 AC: 136 AN: 5182

South Asian (SAS) AF: 0.157 AC: 758 AN: 4822

European-Finnish (FIN) AF: 0.346 AC: 3657 AN: 10568

Middle Eastern (MID) AF: 0.354 AC: 104 AN: 294

European-Non Finnish (NFE) AF: 0.386 AC: 26191 AN: 67936

Other (OTH) AF: 0.328 AC: 692 AN: 2112

Alfa AF: 0.349 Hom.: 12846

Bravo AF: 0.261

Asia WGS AF: 0.0990 AC: 346 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.41
DANN	Benign	0.46
PhyloP100		-0.35

Splicing

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

Other links and lift over

dbSNP: rs13123099; hg19: chr4-100194517;