chr18-38483800-G-A

Variant names:

• chr18-38483800-G-A
• rs4300725
• ENST00000809738.1:n.203+6281C>T

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000809738.1(ENSG00000305237):​n.203+6281C>T variant causes a intron change. The variant allele was found at a frequency of 0.233 in 151,712 control chromosomes in the GnomAD database, including 4,686 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 0.23 (4686 hom., cov: 32)
• Consequence: ENSG00000305237 ENST00000809738.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 5.04
• Publications: 2 publications found

Genes affected

ENSG00000305237 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.27).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.285 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105372074	XR_935392.1	n.204+6281C>T		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000305237	ENST00000809738.1	n.203+6281C>T		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.234 AC: 35423 AN: 151598 Hom.: 4693 Cov.: 32

Gnomad AFR AF: 0.143

Gnomad AMI AF: 0.335

Gnomad AMR AF: 0.206

Gnomad ASJ AF: 0.359

Gnomad EAS AF: 0.00310

Gnomad SAS AF: 0.288

Gnomad FIN AF: 0.311

Gnomad MID AF: 0.363

Gnomad NFE AF: 0.288

Gnomad OTH AF: 0.252

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

GnomAD4 genome AF: 0.233 AC: 35422 AN: 151712 Hom.: 4686 Cov.: 32 AF XY: 0.235 AC XY: 17428 AN XY: 74114

African (AFR) AF: 0.142 AC: 5890 AN: 41362

American (AMR) AF: 0.206 AC: 3140 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.359 AC: 1245 AN: 3472

East Asian (EAS) AF: 0.00310 AC: 16 AN: 5156

South Asian (SAS) AF: 0.288 AC: 1382 AN: 4796

European-Finnish (FIN) AF: 0.311 AC: 3257 AN: 10464

Middle Eastern (MID) AF: 0.342 AC: 100 AN: 292

European-Non Finnish (NFE) AF: 0.288 AC: 19562 AN: 67910

Other (OTH) AF: 0.249 AC: 525 AN: 2106

Alfa AF: 0.271 Hom.: 6323

Bravo AF: 0.220

Asia WGS AF: 0.114 AC: 398 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.27
CADD	Uncertain	24
DANN	Benign	0.71
PhyloP100		5.0

Splicing

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

Other links and lift over

dbSNP: rs4300725; hg19: chr18-36063764;