rs8076673

chr17-78335323-A-G

Variant summary

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

The ENST00000586321.1(ENSG00000267737):n.61-8642A>G 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 0.18 in 151,992 control chromosomes in the GnomAD database, including 2,777 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 0.18 (2777 hom., cov: 32)
• Consequence: ENST00000586321.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.599

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.253 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000586321.1	n.61-8642A>G		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.180 AC: 27324 AN: 151874 Hom.: 2775 Cov.: 32

Gnomad AFR AF: 0.257

Gnomad AMI AF: 0.149

Gnomad AMR AF: 0.151

Gnomad ASJ AF: 0.181

Gnomad EAS AF: 0.00135

Gnomad SAS AF: 0.140

Gnomad FIN AF: 0.115

Gnomad MID AF: 0.121

Gnomad NFE AF: 0.167

Gnomad OTH AF: 0.161

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

GnomAD4 genome AF: 0.180 AC: 27341 AN: 151992 Hom.: 2777 Cov.: 32 AF XY: 0.174 AC XY: 12962 AN XY: 74290

Gnomad4 AFR AF: 0.257

Gnomad4 AMR AF: 0.151

Gnomad4 ASJ AF: 0.181

Gnomad4 EAS AF: 0.00135

Gnomad4 SAS AF: 0.140

Gnomad4 FIN AF: 0.115

Gnomad4 NFE AF: 0.167

Gnomad4 OTH AF: 0.159

Alfa AF: 0.180 Hom.: 335

Bravo AF: 0.185

Asia WGS AF: 0.0700 AC: 247 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	1.7
Dann	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs8076673; hg19: chr17-76331404;