chr17-13394477-C-A

Variant names:

• chr17-13394477-C-A
• rs3944086
• ENST00000767988.1:n.204-7288G>T

Variant summary

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

The ENST00000767988.1(ENSG00000300019):​n.204-7288G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.875 in 152,130 control chromosomes in the GnomAD database, including 58,372 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 0.88 (58372 hom., cov: 32)
• Consequence: ENSG00000300019 ENST00000767988.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.843
• Publications: 3 publications found

Genes affected

ENSG00000300019 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.973 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000300019	ENST00000767988.1	n.204-7288G>T		intron_variant	Intron 1 of 4

Frequencies

GnomAD3 genomes AF: 0.875 AC: 133021 AN: 152012 Hom.: 58334 Cov.: 32

Gnomad AFR AF: 0.828

Gnomad AMI AF: 0.865

Gnomad AMR AF: 0.910

Gnomad ASJ AF: 0.873

Gnomad EAS AF: 0.996

Gnomad SAS AF: 0.817

Gnomad FIN AF: 0.891

Gnomad MID AF: 0.851

Gnomad NFE AF: 0.888

Gnomad OTH AF: 0.881

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

GnomAD4 genome AF: 0.875 AC: 133114 AN: 152130 Hom.: 58372 Cov.: 32 AF XY: 0.875 AC XY: 65063 AN XY: 74356

African (AFR) AF: 0.828 AC: 34348 AN: 41478

American (AMR) AF: 0.910 AC: 13917 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.873 AC: 3028 AN: 3470

East Asian (EAS) AF: 0.996 AC: 5143 AN: 5166

South Asian (SAS) AF: 0.816 AC: 3925 AN: 4808

European-Finnish (FIN) AF: 0.891 AC: 9442 AN: 10598

Middle Eastern (MID) AF: 0.861 AC: 253 AN: 294

European-Non Finnish (NFE) AF: 0.888 AC: 60405 AN: 68004

Other (OTH) AF: 0.883 AC: 1864 AN: 2112

Alfa AF: 0.883 Hom.: 102564

Bravo AF: 0.877

Asia WGS AF: 0.906 AC: 3150 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.67
DANN	Benign	0.26
PhyloP100		-0.84

Splicing

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

Other links and lift over

dbSNP: rs3944086; hg19: chr17-13297794; COSMIC: COSV60074381;