rs2202063

Positions:

• chr18-69299440-T-C

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 0.355 in 151,992 control chromosomes in the GnomAD database, including 9,994 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 0.36 (9994 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.630

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.449 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: 0.355 AC: 53954 AN: 151876 Hom.: 9987 Cov.: 32

Gnomad AFR AF: 0.454

Gnomad AMI AF: 0.418

Gnomad AMR AF: 0.285

Gnomad ASJ AF: 0.356

Gnomad EAS AF: 0.275

Gnomad SAS AF: 0.310

Gnomad FIN AF: 0.285

Gnomad MID AF: 0.430

Gnomad NFE AF: 0.330

Gnomad OTH AF: 0.349

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

GnomAD4 genome AF: 0.355 AC: 53993 AN: 151992 Hom.: 9994 Cov.: 32 AF XY: 0.351 AC XY: 26080 AN XY: 74284

Gnomad4 AFR AF: 0.454

Gnomad4 AMR AF: 0.284

Gnomad4 ASJ AF: 0.356

Gnomad4 EAS AF: 0.276

Gnomad4 SAS AF: 0.310

Gnomad4 FIN AF: 0.285

Gnomad4 NFE AF: 0.330

Gnomad4 OTH AF: 0.346

Alfa AF: 0.356 Hom.: 1250

Bravo AF: 0.356

Asia WGS AF: 0.317 AC: 1101 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.48
DANN	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2202063; hg19: chr18-66966676;