rs1039610

Variant names:

• chr18-78188807-G-A
• rs1039610

Your query was ambiguous. Multiple possible variants found:

• chr18-78188807-G-A
• chr18-78188807-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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;