rs238129

Variant names:

• chr18-3488153-G-A
• rs238129

Your query was ambiguous. Multiple possible variants found:

• chr18-3488153-G-A
• chr18-3488153-G-C
• chr18-3488153-G-T

Variant summary

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

The variant allele was found at a frequency of 0.418 in 151,906 control chromosomes in the GnomAD database, including 13,771 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 0.42 (13771 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.219
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.466 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

Frequencies

GnomAD3 genomes AF: 0.418 AC: 63425 AN: 151788 Hom.: 13760 Cov.: 32

Gnomad AFR AF: 0.406

Gnomad AMI AF: 0.409

Gnomad AMR AF: 0.339

Gnomad ASJ AF: 0.418

Gnomad EAS AF: 0.128

Gnomad SAS AF: 0.208

Gnomad FIN AF: 0.486

Gnomad MID AF: 0.338

Gnomad NFE AF: 0.470

Gnomad OTH AF: 0.399

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

GnomAD4 genome AF: 0.418 AC: 63472 AN: 151906 Hom.: 13771 Cov.: 32 AF XY: 0.409 AC XY: 30379 AN XY: 74236

African (AFR) AF: 0.406 AC: 16835 AN: 41426

American (AMR) AF: 0.338 AC: 5160 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.418 AC: 1451 AN: 3468

East Asian (EAS) AF: 0.128 AC: 663 AN: 5168

South Asian (SAS) AF: 0.208 AC: 1001 AN: 4808

European-Finnish (FIN) AF: 0.486 AC: 5108 AN: 10518

Middle Eastern (MID) AF: 0.339 AC: 99 AN: 292

European-Non Finnish (NFE) AF: 0.470 AC: 31951 AN: 67952

Other (OTH) AF: 0.394 AC: 833 AN: 2114

Alfa AF: 0.439 Hom.: 66645

Bravo AF: 0.407

Asia WGS AF: 0.189 AC: 657 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.8
DANN	Benign	0.42
PhyloP100		-0.22

Splicing

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

Other links and lift over

dbSNP: rs238129; hg19: chr18-3488151;