rs17780102

Variant names:

• chr12-3599443-G-A
• rs17780102

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 0.33 in 152,030 control chromosomes in the GnomAD database, including 8,647 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 0.33 (8647 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.76
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.473 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: 0.330 AC: 50102 AN: 151912 Hom.: 8642 Cov.: 32

Gnomad AFR AF: 0.258

Gnomad AMI AF: 0.379

Gnomad AMR AF: 0.442

Gnomad ASJ AF: 0.275

Gnomad EAS AF: 0.489

Gnomad SAS AF: 0.321

Gnomad FIN AF: 0.304

Gnomad MID AF: 0.229

Gnomad NFE AF: 0.343

Gnomad OTH AF: 0.344

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

GnomAD4 genome AF: 0.330 AC: 50128 AN: 152030 Hom.: 8647 Cov.: 32 AF XY: 0.331 AC XY: 24592 AN XY: 74320

African (AFR) AF: 0.258 AC: 10674 AN: 41450

American (AMR) AF: 0.442 AC: 6754 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.275 AC: 955 AN: 3468

East Asian (EAS) AF: 0.489 AC: 2526 AN: 5168

South Asian (SAS) AF: 0.321 AC: 1546 AN: 4816

European-Finnish (FIN) AF: 0.304 AC: 3215 AN: 10562

Middle Eastern (MID) AF: 0.229 AC: 67 AN: 292

European-Non Finnish (NFE) AF: 0.343 AC: 23324 AN: 67974

Other (OTH) AF: 0.341 AC: 721 AN: 2112

Alfa AF: 0.340 Hom.: 5895

Bravo AF: 0.344

Asia WGS AF: 0.405 AC: 1406 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.069
DANN	Benign	0.62
PhyloP100		-1.8

Splicing

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

Other links and lift over

dbSNP: rs17780102; hg19: chr12-3708609;