rs3213875

chr18-75472093-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.383 in 152,150 control chromosomes in the GnomAD database, including 11,258 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 0.38 (11258 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.120

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.445 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.383 AC: 58285 AN: 152032 Hom.: 11250 Cov.: 32

Gnomad AFR AF: 0.344

Gnomad AMI AF: 0.271

Gnomad AMR AF: 0.349

Gnomad ASJ AF: 0.447

Gnomad EAS AF: 0.448

Gnomad SAS AF: 0.462

Gnomad FIN AF: 0.449

Gnomad MID AF: 0.478

Gnomad NFE AF: 0.391

Gnomad OTH AF: 0.420

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

GnomAD4 genome AF: 0.383 AC: 58310 AN: 152150 Hom.: 11258 Cov.: 32 AF XY: 0.387 AC XY: 28796 AN XY: 74392

Gnomad4 AFR AF: 0.344

Gnomad4 AMR AF: 0.348

Gnomad4 ASJ AF: 0.447

Gnomad4 EAS AF: 0.448

Gnomad4 SAS AF: 0.461

Gnomad4 FIN AF: 0.449

Gnomad4 NFE AF: 0.391

Gnomad4 OTH AF: 0.419

Alfa AF: 0.381 Hom.: 2650

Bravo AF: 0.372

Asia WGS AF: 0.446 AC: 1549 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	2.6
Dann	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3213875; hg19: chr18-73184048;