rs1577792

Variant names:

• chr6-79176360-A-G
• rs1577792
• ENST00000759658.1:n.317-25484A>G

Your query was ambiguous. Multiple possible variants found:

• chr6-79176360-A-G
• chr6-79176360-A-T

Variant summary

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

The ENST00000759658.1(ENSG00000286340):​n.317-25484A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.554 in 152,040 control chromosomes in the GnomAD database, including 24,707 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 0.55 (24707 hom., cov: 32)
• Consequence: ENSG00000286340 ENST00000759658.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.274
• Publications: 2 publications found

Genes affected

ENSG00000286340 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.82 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000759658.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000286340	ENST00000759658.1		n.317-25484A>G		intron	N/A
	ENSG00000286340	ENST00000759659.1		n.179-4127A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.554 AC: 84197 AN: 151922 Hom.: 24691 Cov.: 32

Gnomad AFR AF: 0.373

Gnomad AMI AF: 0.635

Gnomad AMR AF: 0.709

Gnomad ASJ AF: 0.590

Gnomad EAS AF: 0.841

Gnomad SAS AF: 0.655

Gnomad FIN AF: 0.572

Gnomad MID AF: 0.535

Gnomad NFE AF: 0.594

Gnomad OTH AF: 0.601

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

GnomAD4 genome AF: 0.554 AC: 84246 AN: 152040 Hom.: 24707 Cov.: 32 AF XY: 0.558 AC XY: 41474 AN XY: 74310

African (AFR) AF: 0.373 AC: 15465 AN: 41462

American (AMR) AF: 0.709 AC: 10832 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.590 AC: 2046 AN: 3470

East Asian (EAS) AF: 0.841 AC: 4349 AN: 5174

South Asian (SAS) AF: 0.655 AC: 3152 AN: 4814

European-Finnish (FIN) AF: 0.572 AC: 6040 AN: 10564

Middle Eastern (MID) AF: 0.541 AC: 158 AN: 292

European-Non Finnish (NFE) AF: 0.594 AC: 40351 AN: 67972

Other (OTH) AF: 0.604 AC: 1275 AN: 2112

Alfa AF: 0.585 Hom.: 21319

Bravo AF: 0.559

Asia WGS AF: 0.723 AC: 2515 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	7.2
DANN	Benign	0.90
PhyloP100		-0.27

Splicing

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

Other links and lift over

dbSNP: rs1577792; hg19: chr6-79886077;