rs1830206

Variant names:

• chr10-36956778-G-A
• rs1830206

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 0.593 in 151,988 control chromosomes in the GnomAD database, including 31,098 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 0.59 (31098 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.650
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.757 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: 0.593 AC: 90130 AN: 151870 Hom.: 31094 Cov.: 32

Gnomad AFR AF: 0.232

Gnomad AMI AF: 0.822

Gnomad AMR AF: 0.737

Gnomad ASJ AF: 0.692

Gnomad EAS AF: 0.369

Gnomad SAS AF: 0.544

Gnomad FIN AF: 0.782

Gnomad MID AF: 0.734

Gnomad NFE AF: 0.763

Gnomad OTH AF: 0.634

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

GnomAD4 genome AF: 0.593 AC: 90139 AN: 151988 Hom.: 31098 Cov.: 32 AF XY: 0.594 AC XY: 44110 AN XY: 74282

African (AFR) AF: 0.231 AC: 9581 AN: 41456

American (AMR) AF: 0.737 AC: 11239 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.692 AC: 2400 AN: 3468

East Asian (EAS) AF: 0.368 AC: 1896 AN: 5148

South Asian (SAS) AF: 0.545 AC: 2625 AN: 4820

European-Finnish (FIN) AF: 0.782 AC: 8275 AN: 10584

Middle Eastern (MID) AF: 0.738 AC: 217 AN: 294

European-Non Finnish (NFE) AF: 0.763 AC: 51820 AN: 67946

Other (OTH) AF: 0.633 AC: 1336 AN: 2110

Alfa AF: 0.707 Hom.: 165126

Bravo AF: 0.575

Asia WGS AF: 0.462 AC: 1604 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.34
DANN	Benign	0.36
PhyloP100		-0.65

Splicing

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

Other links and lift over

dbSNP: rs1830206; hg19: chr10-37245706;