rs3901727

Variant names:

• chr18-29792308-C-A
• rs3901727
• ENST00000803180.1:n.250+30024G>T

Variant summary

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

The ENST00000803180.1(ENSG00000304402):​n.250+30024G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.177 in 152,052 control chromosomes in the GnomAD database, including 2,746 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 0.18 (2746 hom., cov: 32)
• Consequence: ENSG00000304402 ENST00000803180.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.230
• Publications: 1 publications found

Genes affected

ENSG00000304402 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.69).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.224 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000304402	ENST00000803180.1	n.250+30024G>T		intron_variant	Intron 2 of 2
ENSG00000304402	ENST00000803181.1	n.250+30024G>T		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.177 AC: 26907 AN: 151934 Hom.: 2741 Cov.: 32

Gnomad AFR AF: 0.0813

Gnomad AMI AF: 0.261

Gnomad AMR AF: 0.189

Gnomad ASJ AF: 0.204

Gnomad EAS AF: 0.0828

Gnomad SAS AF: 0.186

Gnomad FIN AF: 0.246

Gnomad MID AF: 0.171

Gnomad NFE AF: 0.227

Gnomad OTH AF: 0.161

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

GnomAD4 genome AF: 0.177 AC: 26911 AN: 152052 Hom.: 2746 Cov.: 32 AF XY: 0.177 AC XY: 13126 AN XY: 74316

African (AFR) AF: 0.0812 AC: 3369 AN: 41488

American (AMR) AF: 0.189 AC: 2894 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.204 AC: 709 AN: 3470

East Asian (EAS) AF: 0.0828 AC: 427 AN: 5160

South Asian (SAS) AF: 0.185 AC: 893 AN: 4820

European-Finnish (FIN) AF: 0.246 AC: 2592 AN: 10550

Middle Eastern (MID) AF: 0.167 AC: 49 AN: 294

European-Non Finnish (NFE) AF: 0.227 AC: 15408 AN: 67974

Other (OTH) AF: 0.158 AC: 333 AN: 2110

Alfa AF: 0.203 Hom.: 1820

Bravo AF: 0.167

Asia WGS AF: 0.112 AC: 387 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.69
CADD	Benign	3.4
DANN	Benign	0.84
PhyloP100		-0.23

Splicing

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

Other links and lift over

dbSNP: rs3901727; hg19: chr18-27372273;