rs3828541

Variant names:

• chr4-99121111-A-G
• rs3828541
• ENST00000500358.6:n.429-12444A>G

Variant summary

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

The ENST00000500358.6(ENSG00000246090):​n.429-12444A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.387 in 152,050 control chromosomes in the GnomAD database, including 11,941 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 0.39 (11941 hom., cov: 32)
• Consequence: ENSG00000246090 ENST00000500358.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.821
• Publications: 14 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=-0.87).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.485 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC100507053	NR_037884.1	n.429-12444A>G		intron_variant	Intron 1 of 9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000246090	ENST00000500358.6	n.429-12444A>G		intron_variant	Intron 1 of 9	1
ENSG00000246090	ENST00000661393.1	n.426-12444A>G		intron_variant	Intron 1 of 9
ENSG00000246090	ENST00000670724.2	n.481-12444A>G		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.387 AC: 58746 AN: 151932 Hom.: 11929 Cov.: 32

Gnomad AFR AF: 0.298

Gnomad AMI AF: 0.395

Gnomad AMR AF: 0.349

Gnomad ASJ AF: 0.394

Gnomad EAS AF: 0.124

Gnomad SAS AF: 0.501

Gnomad FIN AF: 0.463

Gnomad MID AF: 0.465

Gnomad NFE AF: 0.449

Gnomad OTH AF: 0.386

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

GnomAD4 genome AF: 0.387 AC: 58782 AN: 152050 Hom.: 11941 Cov.: 32 AF XY: 0.387 AC XY: 28787 AN XY: 74314

African (AFR) AF: 0.298 AC: 12349 AN: 41492

American (AMR) AF: 0.349 AC: 5327 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.394 AC: 1368 AN: 3472

East Asian (EAS) AF: 0.123 AC: 639 AN: 5178

South Asian (SAS) AF: 0.501 AC: 2415 AN: 4816

European-Finnish (FIN) AF: 0.463 AC: 4876 AN: 10542

Middle Eastern (MID) AF: 0.455 AC: 133 AN: 292

European-Non Finnish (NFE) AF: 0.449 AC: 30491 AN: 67960

Other (OTH) AF: 0.389 AC: 824 AN: 2116

Alfa AF: 0.420 Hom.: 34496

Bravo AF: 0.369

Asia WGS AF: 0.380 AC: 1324 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	3.5
DANN	Benign	0.51
PhyloP100		0.82

Splicing

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

Other links and lift over

dbSNP: rs3828541; hg19: chr4-100042262;