chr18-60543727-C-G

Variant names:

• chr18-60543727-C-G
• rs547363

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 0.593 in 152,022 control chromosomes in the GnomAD database, including 27,475 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 0.59 (27475 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.316
• Publications: 1 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 (AFR) allele frequency at 95% confidence interval = 0.736 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: 0.593 AC: 90017 AN: 151904 Hom.: 27421 Cov.: 32

Gnomad AFR AF: 0.742

Gnomad AMI AF: 0.609

Gnomad AMR AF: 0.517

Gnomad ASJ AF: 0.543

Gnomad EAS AF: 0.672

Gnomad SAS AF: 0.490

Gnomad FIN AF: 0.497

Gnomad MID AF: 0.430

Gnomad NFE AF: 0.538

Gnomad OTH AF: 0.578

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

GnomAD4 genome AF: 0.593 AC: 90131 AN: 152022 Hom.: 27475 Cov.: 32 AF XY: 0.589 AC XY: 43795 AN XY: 74306

African (AFR) AF: 0.743 AC: 30810 AN: 41490

American (AMR) AF: 0.517 AC: 7888 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.543 AC: 1884 AN: 3470

East Asian (EAS) AF: 0.672 AC: 3466 AN: 5156

South Asian (SAS) AF: 0.494 AC: 2379 AN: 4818

European-Finnish (FIN) AF: 0.497 AC: 5250 AN: 10560

Middle Eastern (MID) AF: 0.442 AC: 130 AN: 294

European-Non Finnish (NFE) AF: 0.538 AC: 36546 AN: 67938

Other (OTH) AF: 0.578 AC: 1223 AN: 2116

Alfa AF: 0.579 Hom.: 3204

Bravo AF: 0.604

Asia WGS AF: 0.586 AC: 2042 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	0.85
DANN	Benign	0.48
PhyloP100		-0.32

Splicing

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

Other links and lift over

dbSNP: rs547363; hg19: chr18-58210960;