rs1039610

chr18-78188807-G-Achr18-78188807-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 0.682 in 150,452 control chromosomes in the GnomAD database, including 35,151 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 0.68 (35151 hom., cov: 25)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.830

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.722 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: 0.682 AC: 102505 AN: 150330 Hom.: 35126 Cov.: 25

Gnomad AFR AF: 0.680

Gnomad AMI AF: 0.756

Gnomad AMR AF: 0.677

Gnomad ASJ AF: 0.758

Gnomad EAS AF: 0.489

Gnomad SAS AF: 0.742

Gnomad FIN AF: 0.638

Gnomad MID AF: 0.721

Gnomad NFE AF: 0.695

Gnomad OTH AF: 0.692

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

GnomAD4 genome AF: 0.682 AC: 102582 AN: 150452 Hom.: 35151 Cov.: 25 AF XY: 0.680 AC XY: 49938 AN XY: 73442

Gnomad4 AFR AF: 0.680

Gnomad4 AMR AF: 0.677

Gnomad4 ASJ AF: 0.758

Gnomad4 EAS AF: 0.490

Gnomad4 SAS AF: 0.742

Gnomad4 FIN AF: 0.638

Gnomad4 NFE AF: 0.695

Gnomad4 OTH AF: 0.690

Alfa AF: 0.700 Hom.: 16919

Bravo AF: 0.680

Asia WGS AF: 0.646 AC: 2248 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	0.49
Dann	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1039610; hg19: chr18-75948807;