rs17038828

Variant names:

• chr3-39433851-C-T
• rs17038828
• ENST00000772824.1:n.638G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000772824.1(ENSG00000286781):​n.638G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0729 in 152,290 control chromosomes in the GnomAD database, including 878 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 0.073 (878 hom., cov: 32)
• Consequence: ENSG00000286781 ENST00000772824.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.220
• Publications: 6 publications found

Genes affected

ENSG00000286781 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.71).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.194 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000772824.1. You can select a different transcript below to see updated ACMG assignments.

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
	ENSG00000286781	ENST00000772824.1		n.638G>A		non_coding_transcript_exon	Exon 2 of 2
	ENSG00000286781	ENST00000772825.1		n.462G>A		non_coding_transcript_exon	Exon 3 of 3
	ENSG00000286781	ENST00000772826.1		n.790G>A		non_coding_transcript_exon	Exon 2 of 2

Frequencies

GnomAD3 genomes AF: 0.0727 AC: 11069 AN: 152172 Hom.: 873 Cov.: 32

Gnomad AFR AF: 0.197

Gnomad AMI AF: 0.0888

Gnomad AMR AF: 0.0428

Gnomad ASJ AF: 0.0135

Gnomad EAS AF: 0.0521

Gnomad SAS AF: 0.0335

Gnomad FIN AF: 0.0165

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.0200

Gnomad OTH AF: 0.0632

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

GnomAD4 genome AF: 0.0729 AC: 11107 AN: 152290 Hom.: 878 Cov.: 32 AF XY: 0.0721 AC XY: 5368 AN XY: 74476

African (AFR) AF: 0.198 AC: 8210 AN: 41526

American (AMR) AF: 0.0428 AC: 655 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.0135 AC: 47 AN: 3470

East Asian (EAS) AF: 0.0520 AC: 270 AN: 5192

South Asian (SAS) AF: 0.0338 AC: 163 AN: 4826

European-Finnish (FIN) AF: 0.0165 AC: 175 AN: 10628

Middle Eastern (MID) AF: 0.0408 AC: 12 AN: 294

European-Non Finnish (NFE) AF: 0.0200 AC: 1362 AN: 68024

Other (OTH) AF: 0.0625 AC: 132 AN: 2112

Alfa AF: 0.0542 Hom.: 188

Bravo AF: 0.0830

Asia WGS AF: 0.0500 AC: 176 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.71
CADD	Benign	11
DANN	Benign	0.89
PhyloP100		0.22

Splicing

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

Other links and lift over

dbSNP: rs17038828; hg19: chr3-39475342;