rs2602836

Variant names:

• chr4-99093654-A-G
• rs2602836
• ENST00000500358.6:n.428+4370A>G

Variant summary

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

The ENST00000500358.6(ENSG00000246090):​n.428+4370A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.509 in 152,074 control chromosomes in the GnomAD database, including 21,086 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 0.51 (21086 hom., cov: 33)
• Consequence: ENSG00000246090 ENST00000500358.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.233
• Publications: 69 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=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.837 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC100507053	NR_037884.1	n.428+4370A>G		intron_variant	Intron 1 of 9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000246090	ENST00000500358.6	n.428+4370A>G		intron_variant	Intron 1 of 9	1
ENSG00000246090	ENST00000499178.3	n.415+4370A>G		intron_variant	Intron 1 of 2	3
ENSG00000246090	ENST00000661393.1	n.425+4370A>G		intron_variant	Intron 1 of 9

Frequencies

GnomAD3 genomes AF: 0.509 AC: 77355 AN: 151954 Hom.: 21083 Cov.: 33

Gnomad AFR AF: 0.331

Gnomad AMI AF: 0.601

Gnomad AMR AF: 0.455

Gnomad ASJ AF: 0.569

Gnomad EAS AF: 0.858

Gnomad SAS AF: 0.793

Gnomad FIN AF: 0.533

Gnomad MID AF: 0.646

Gnomad NFE AF: 0.574

Gnomad OTH AF: 0.522

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

GnomAD4 genome AF: 0.509 AC: 77373 AN: 152074 Hom.: 21086 Cov.: 33 AF XY: 0.515 AC XY: 38260 AN XY: 74324

African (AFR) AF: 0.331 AC: 13718 AN: 41486

American (AMR) AF: 0.455 AC: 6946 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.569 AC: 1974 AN: 3470

East Asian (EAS) AF: 0.858 AC: 4441 AN: 5174

South Asian (SAS) AF: 0.792 AC: 3821 AN: 4822

European-Finnish (FIN) AF: 0.533 AC: 5624 AN: 10556

Middle Eastern (MID) AF: 0.636 AC: 187 AN: 294

European-Non Finnish (NFE) AF: 0.574 AC: 39002 AN: 67974

Other (OTH) AF: 0.526 AC: 1112 AN: 2116

Alfa AF: 0.562 Hom.: 112400

Bravo AF: 0.488

Asia WGS AF: 0.749 AC: 2602 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	3.8
DANN	Benign	0.33
PhyloP100		0.23

Splicing

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

Other links and lift over

dbSNP: rs2602836; hg19: chr4-100014805;