rs10514033

chr18-72044019-G-Achr18-72044019-G-T

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 0.0311 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.0522

Gnomad4 AMR AF: 0.0417

Gnomad4 ASJ AF: 0.00317

Gnomad4 EAS AF: 0.0327

Gnomad4 SAS AF: 0.00540

Gnomad4 FIN AF: 0.0305

Gnomad4 NFE AF: 0.0195

Gnomad4 OTH AF: 0.0222

Alfa AF: 0.0167 Hom.: 5

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10514033; hg19: chr18-69711254;