rs17027938

Variant names:

• chr3-86733823-A-G
• rs17027938
• ENST00000760372.1:n.235+16296A>G

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000760372.1(ENSG00000299083):​n.235+16296A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.118 in 152,198 control chromosomes in the GnomAD database, including 2,173 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 0.12 (2173 hom., cov: 33)
• Consequence: ENSG00000299083 ENST00000760372.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.88
• Publications: 1 publications found

Genes affected

ENSG00000299083 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.44).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.456 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC101927518	XR_941027.4	n.269-3355A>G		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000299083	ENST00000760372.1	n.235+16296A>G		intron_variant	Intron 2 of 3
ENSG00000299083	ENST00000760373.1	n.277-3355A>G		intron_variant	Intron 2 of 2
ENSG00000299083	ENST00000760374.1	n.331-3355A>G		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.118 AC: 17947 AN: 152080 Hom.: 2148 Cov.: 33

Gnomad AFR AF: 0.229

Gnomad AMI AF: 0.00219

Gnomad AMR AF: 0.218

Gnomad ASJ AF: 0.0225

Gnomad EAS AF: 0.471

Gnomad SAS AF: 0.0915

Gnomad FIN AF: 0.0470

Gnomad MID AF: 0.0316

Gnomad NFE AF: 0.0212

Gnomad OTH AF: 0.113

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

GnomAD4 genome AF: 0.118 AC: 18015 AN: 152198 Hom.: 2173 Cov.: 33 AF XY: 0.123 AC XY: 9129 AN XY: 74410

African (AFR) AF: 0.230 AC: 9534 AN: 41520

American (AMR) AF: 0.218 AC: 3336 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.0225 AC: 78 AN: 3468

East Asian (EAS) AF: 0.471 AC: 2431 AN: 5158

South Asian (SAS) AF: 0.0912 AC: 440 AN: 4826

European-Finnish (FIN) AF: 0.0470 AC: 499 AN: 10618

Middle Eastern (MID) AF: 0.0238 AC: 7 AN: 294

European-Non Finnish (NFE) AF: 0.0212 AC: 1442 AN: 68004

Other (OTH) AF: 0.116 AC: 246 AN: 2114

Alfa AF: 0.0594 Hom.: 2853

Bravo AF: 0.140

Asia WGS AF: 0.272 AC: 944 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.44
CADD	Benign	16
DANN	Benign	0.54
PhyloP100		1.9

Splicing

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

Other links and lift over

dbSNP: rs17027938; hg19: chr3-86782973; COSMIC: COSV107175647;