17-78325952-A-T

Variant names:

• chr17-78325952-A-T
• rs4789575
• ENST00000586321.1:n.60+10164A>T

Variant summary

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

The ENST00000586321.1(ENSG00000267737):​n.60+10164A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.86 in 152,256 control chromosomes in the GnomAD database, including 56,621 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 0.86 (56621 hom., cov: 33)
• Consequence: ENSG00000267737 ENST00000586321.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.59
• Publications: 4 publications found

Genes affected

ENSG00000267737 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.06).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.966 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105371912	NR_188632.1	n.73+10164A>T		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000267737	ENST00000586321.1	n.60+10164A>T		intron_variant	Intron 1 of 2	3
ENSG00000267737	ENST00000823930.1	n.38+10164A>T		intron_variant	Intron 1 of 1
ENSG00000267737	ENST00000823931.1	n.71+7964A>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.860 AC: 130788 AN: 152138 Hom.: 56554 Cov.: 33

Gnomad AFR AF: 0.949

Gnomad AMI AF: 0.841

Gnomad AMR AF: 0.861

Gnomad ASJ AF: 0.730

Gnomad EAS AF: 0.988

Gnomad SAS AF: 0.865

Gnomad FIN AF: 0.825

Gnomad MID AF: 0.785

Gnomad NFE AF: 0.808

Gnomad OTH AF: 0.827

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

GnomAD4 genome AF: 0.860 AC: 130915 AN: 152256 Hom.: 56621 Cov.: 33 AF XY: 0.861 AC XY: 64111 AN XY: 74442

African (AFR) AF: 0.949 AC: 39431 AN: 41552

American (AMR) AF: 0.861 AC: 13172 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.730 AC: 2533 AN: 3468

East Asian (EAS) AF: 0.988 AC: 5125 AN: 5186

South Asian (SAS) AF: 0.865 AC: 4168 AN: 4818

European-Finnish (FIN) AF: 0.825 AC: 8759 AN: 10612

Middle Eastern (MID) AF: 0.789 AC: 232 AN: 294

European-Non Finnish (NFE) AF: 0.808 AC: 54984 AN: 68012

Other (OTH) AF: 0.828 AC: 1747 AN: 2110

Alfa AF: 0.828 Hom.: 6109

Bravo AF: 0.866

Asia WGS AF: 0.920 AC: 3199 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.024
DANN	Benign	0.36
PhyloP100		-2.6

Splicing

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

Other links and lift over

dbSNP: rs4789575; hg19: chr17-76322033;