rs729053

Variant names:

• chr18-55142450-G-C
• rs729053

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 0.265 in 151,960 control chromosomes in the GnomAD database, including 6,210 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 0.27 (6210 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.514
• Publications: 3 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 = 0.362 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: 0.265 AC: 40275 AN: 151842 Hom.: 6201 Cov.: 32

Gnomad AFR AF: 0.0923

Gnomad AMI AF: 0.241

Gnomad AMR AF: 0.329

Gnomad ASJ AF: 0.369

Gnomad EAS AF: 0.265

Gnomad SAS AF: 0.377

Gnomad FIN AF: 0.301

Gnomad MID AF: 0.245

Gnomad NFE AF: 0.337

Gnomad OTH AF: 0.297

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

GnomAD4 genome AF: 0.265 AC: 40288 AN: 151960 Hom.: 6210 Cov.: 32 AF XY: 0.264 AC XY: 19636 AN XY: 74276

African (AFR) AF: 0.0920 AC: 3817 AN: 41480

American (AMR) AF: 0.329 AC: 5023 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.369 AC: 1280 AN: 3470

East Asian (EAS) AF: 0.265 AC: 1360 AN: 5134

South Asian (SAS) AF: 0.376 AC: 1811 AN: 4812

European-Finnish (FIN) AF: 0.301 AC: 3187 AN: 10582

Middle Eastern (MID) AF: 0.240 AC: 70 AN: 292

European-Non Finnish (NFE) AF: 0.337 AC: 22880 AN: 67924

Other (OTH) AF: 0.304 AC: 640 AN: 2104

Alfa AF: 0.286 Hom.: 857

Bravo AF: 0.258

Asia WGS AF: 0.339 AC: 1176 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	2.2
DANN	Benign	0.38
PhyloP100		0.51

Splicing

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

Other links and lift over

dbSNP: rs729053; hg19: chr18-52809681;