chr17-51175780-G-A

Variant names:

• chr17-51175780-G-A
• rs12942155

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 0.489 in 151,478 control chromosomes in the GnomAD database, including 18,409 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 0.49 (18409 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.537 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: 0.489 AC: 74074 AN: 151362 Hom.: 18403 Cov.: 30

Gnomad AFR AF: 0.544

Gnomad AMI AF: 0.509

Gnomad AMR AF: 0.503

Gnomad ASJ AF: 0.357

Gnomad EAS AF: 0.390

Gnomad SAS AF: 0.348

Gnomad FIN AF: 0.473

Gnomad MID AF: 0.385

Gnomad NFE AF: 0.481

Gnomad OTH AF: 0.474

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

GnomAD4 genome AF: 0.489 AC: 74111 AN: 151478 Hom.: 18409 Cov.: 30 AF XY: 0.483 AC XY: 35765 AN XY: 74002

African (AFR) AF: 0.543 AC: 22406 AN: 41262

American (AMR) AF: 0.503 AC: 7665 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.357 AC: 1232 AN: 3454

East Asian (EAS) AF: 0.389 AC: 1987 AN: 5104

South Asian (SAS) AF: 0.349 AC: 1672 AN: 4790

European-Finnish (FIN) AF: 0.473 AC: 4957 AN: 10470

Middle Eastern (MID) AF: 0.377 AC: 110 AN: 292

European-Non Finnish (NFE) AF: 0.481 AC: 32620 AN: 67856

Other (OTH) AF: 0.476 AC: 1001 AN: 2102

Alfa AF: 0.490 Hom.: 9236

Bravo AF: 0.497

Asia WGS AF: 0.402 AC: 1395 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	6.2
DANN	Benign	0.63
PhyloP100		0.0

Splicing

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

Other links and lift over

dbSNP: rs12942155; hg19: chr17-49253141;