17-78325952-A-T

Position:

• chr17-78325952-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000586321.1(ENSG00000267737):​n.60+10164A>T variant causes a intron, non coding transcript 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: ENST00000586321.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.59

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000586321.1	n.60+10164A>T		intron_variant, non_coding_transcript_variant		3

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

Gnomad4 AFR AF: 0.949

Gnomad4 AMR AF: 0.861

Gnomad4 ASJ AF: 0.730

Gnomad4 EAS AF: 0.988

Gnomad4 SAS AF: 0.865

Gnomad4 FIN AF: 0.825

Gnomad4 NFE AF: 0.808

Gnomad4 OTH AF: 0.828

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4789575; hg19: chr17-76322033;