rs4450508

Variant names:

• chr18-60246201-G-A
• rs4450508

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 0.312 in 152,056 control chromosomes in the GnomAD database, including 7,666 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 0.31 (7666 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.858
• Publications: 18 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.421 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: 0.312 AC: 47409 AN: 151938 Hom.: 7661 Cov.: 33

Gnomad AFR AF: 0.288

Gnomad AMI AF: 0.403

Gnomad AMR AF: 0.232

Gnomad ASJ AF: 0.278

Gnomad EAS AF: 0.164

Gnomad SAS AF: 0.436

Gnomad FIN AF: 0.333

Gnomad MID AF: 0.377

Gnomad NFE AF: 0.345

Gnomad OTH AF: 0.299

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

GnomAD4 genome AF: 0.312 AC: 47424 AN: 152056 Hom.: 7666 Cov.: 33 AF XY: 0.311 AC XY: 23139 AN XY: 74332

African (AFR) AF: 0.287 AC: 11916 AN: 41452

American (AMR) AF: 0.231 AC: 3537 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.278 AC: 963 AN: 3470

East Asian (EAS) AF: 0.163 AC: 846 AN: 5182

South Asian (SAS) AF: 0.437 AC: 2108 AN: 4824

European-Finnish (FIN) AF: 0.333 AC: 3521 AN: 10568

Middle Eastern (MID) AF: 0.371 AC: 109 AN: 294

European-Non Finnish (NFE) AF: 0.345 AC: 23427 AN: 67958

Other (OTH) AF: 0.299 AC: 630 AN: 2104

Alfa AF: 0.330 Hom.: 21177

Bravo AF: 0.300

Asia WGS AF: 0.265 AC: 923 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	1.4
DANN	Benign	0.75
PhyloP100		-0.86

Splicing

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

Other links and lift over

dbSNP: rs4450508; hg19: chr18-57913434;