18-72044019-G-A

Variant names:

• chr18-72044019-G-A
• rs10514033

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 0.0311 in 151,958 control chromosomes in the GnomAD database, including 102 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 0.031 (102 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.523
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0504 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: 0.0310 AC: 4707 AN: 151842 Hom.: 101 Cov.: 32

Gnomad AFR AF: 0.0523

Gnomad AMI AF: 0.0241

Gnomad AMR AF: 0.0413

Gnomad ASJ AF: 0.00317

Gnomad EAS AF: 0.0326

Gnomad SAS AF: 0.00518

Gnomad FIN AF: 0.0305

Gnomad MID AF: 0.00633

Gnomad NFE AF: 0.0195

Gnomad OTH AF: 0.0215

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

GnomAD4 genome AF: 0.0311 AC: 4721 AN: 151958 Hom.: 102 Cov.: 32 AF XY: 0.0306 AC XY: 2272 AN XY: 74260

African (AFR) AF: 0.0522 AC: 2164 AN: 41438

American (AMR) AF: 0.0417 AC: 635 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.00317 AC: 11 AN: 3466

East Asian (EAS) AF: 0.0327 AC: 169 AN: 5168

South Asian (SAS) AF: 0.00540 AC: 26 AN: 4818

European-Finnish (FIN) AF: 0.0305 AC: 323 AN: 10576

Middle Eastern (MID) AF: 0.00680 AC: 2 AN: 294

European-Non Finnish (NFE) AF: 0.0195 AC: 1322 AN: 67928

Other (OTH) AF: 0.0222 AC: 47 AN: 2114

Alfa AF: 0.0209 Hom.: 25

Bravo AF: 0.0334

Asia WGS AF: 0.0260 AC: 91 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.5
DANN	Benign	0.72
PhyloP100		0.52

Splicing

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

Other links and lift over

dbSNP: rs10514033; hg19: chr18-69711254;