rs4300725

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:58979):

LOC105372074 (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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000809738.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000305237	ENST00000809738.1		n.203+6281C>T		intron	N/A

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 v4.9

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs4300725;

hg19: chr18-36063764;