17-38833557-G-A

Variant names:

• chr17-38833557-G-A
• rs228269

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 0.244 in 152,052 control chromosomes in the GnomAD database, including 4,618 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 0.24 (4618 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.22
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.74).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.295 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.244 AC: 37112 AN: 151934 Hom.: 4618 Cov.: 32

Gnomad AFR AF: 0.243

Gnomad AMI AF: 0.405

Gnomad AMR AF: 0.302

Gnomad ASJ AF: 0.268

Gnomad EAS AF: 0.226

Gnomad SAS AF: 0.213

Gnomad FIN AF: 0.178

Gnomad MID AF: 0.184

Gnomad NFE AF: 0.243

Gnomad OTH AF: 0.243

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

GnomAD4 genome AF: 0.244 AC: 37139 AN: 152052 Hom.: 4618 Cov.: 32 AF XY: 0.240 AC XY: 17850 AN XY: 74314

African (AFR) AF: 0.243 AC: 10073 AN: 41470

American (AMR) AF: 0.302 AC: 4598 AN: 15236

Ashkenazi Jewish (ASJ) AF: 0.268 AC: 930 AN: 3470

East Asian (EAS) AF: 0.226 AC: 1165 AN: 5162

South Asian (SAS) AF: 0.213 AC: 1026 AN: 4826

European-Finnish (FIN) AF: 0.178 AC: 1883 AN: 10602

Middle Eastern (MID) AF: 0.177 AC: 52 AN: 294

European-Non Finnish (NFE) AF: 0.243 AC: 16522 AN: 67970

Other (OTH) AF: 0.247 AC: 521 AN: 2110

Alfa AF: 0.236 Hom.: 605

Bravo AF: 0.254

Asia WGS AF: 0.231 AC: 804 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.74
CADD	Benign	0.26
DANN	Benign	0.23
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs228269; hg19: chr17-36989810;