chr18-69299440-T-C

Variant names:

• chr18-69299440-T-C
• rs2202063

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 0.355 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
• Publications: 0 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.454 AC: 18821 AN: 41458

American (AMR) AF: 0.284 AC: 4339 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.356 AC: 1235 AN: 3468

East Asian (EAS) AF: 0.276 AC: 1421 AN: 5154

South Asian (SAS) AF: 0.310 AC: 1496 AN: 4820

European-Finnish (FIN) AF: 0.285 AC: 3014 AN: 10582

Middle Eastern (MID) AF: 0.422 AC: 124 AN: 294

European-Non Finnish (NFE) AF: 0.330 AC: 22432 AN: 67942

Other (OTH) AF: 0.346 AC: 731 AN: 2112

Alfa AF: 0.360 Hom.: 1332

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
PhyloP100		-0.63

Splicing

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

Other links and lift over

dbSNP: rs2202063; hg19: chr18-66966676;