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. The variant received -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
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.680 AC: 27886 AN: 41034

American (AMR) AF: 0.677 AC: 10275 AN: 15172

Ashkenazi Jewish (ASJ) AF: 0.758 AC: 2623 AN: 3460

East Asian (EAS) AF: 0.490 AC: 2385 AN: 4868

South Asian (SAS) AF: 0.742 AC: 3456 AN: 4656

European-Finnish (FIN) AF: 0.638 AC: 6667 AN: 10448

Middle Eastern (MID) AF: 0.722 AC: 208 AN: 288

European-Non Finnish (NFE) AF: 0.695 AC: 46948 AN: 67520

Other (OTH) AF: 0.690 AC: 1446 AN: 2096

Alfa AF: 0.700 Hom.: 18980

Bravo AF: 0.680

Asia WGS AF: 0.646 AC: 2248 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.49
DANN	Benign	0.42
PhyloP100		-0.83

Splicing

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

Other links and lift over

dbSNP: rs1039610; hg19: chr18-75948807;