ENST00000829864.1:n.273+1975A>G

Variant names:

• chr6-32476184-A-G
• rs6457594
• ENST00000829864.1:n.273+1975A>G

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

The ENST00000829864.1(ENSG00000307923):​n.273+1975A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. 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 0.68 (28162 hom., cov: 39)
  • Failed GnomAD Quality Control
• Consequence: ENSG00000307923 ENST00000829864.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.99
• Publications: 7 publications found

Genes affected

ENSG00000307923 (HGNC:):

ACMG classification

Our verdict: Likely_benign. The variant received -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000829864.1. 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
	ENSG00000307923	ENST00000829864.1		n.273+1975A>G		intron	N/A
	ENSG00000307923	ENST00000829865.1		n.269+1975A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.676 AC: 100097 AN: 148098 Hom.: 28143 Cov.: 39

Gnomad AFR AF: 0.615

Gnomad AMI AF: 0.753

Gnomad AMR AF: 0.713

Gnomad ASJ AF: 0.720

Gnomad EAS AF: 0.610

Gnomad SAS AF: 0.634

Gnomad FIN AF: 0.784

Gnomad MID AF: 0.643

Gnomad NFE AF: 0.691

Gnomad OTH AF: 0.684

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

GnomAD4 genome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.676 AC: 100165 AN: 148212 Hom.: 28162 Cov.: 39 AF XY: 0.677 AC XY: 49095 AN XY: 72470

African (AFR) AF: 0.615 AC: 24451 AN: 39754

American (AMR) AF: 0.714 AC: 10713 AN: 15014

Ashkenazi Jewish (ASJ) AF: 0.720 AC: 2473 AN: 3436

East Asian (EAS) AF: 0.611 AC: 3065 AN: 5016

South Asian (SAS) AF: 0.635 AC: 2992 AN: 4714

European-Finnish (FIN) AF: 0.784 AC: 8171 AN: 10420

Middle Eastern (MID) AF: 0.640 AC: 187 AN: 292

European-Non Finnish (NFE) AF: 0.691 AC: 46042 AN: 66612

Other (OTH) AF: 0.678 AC: 1393 AN: 2054

Alfa AF: 0.671 Hom.: 3090

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.3
DANN	Benign	0.50
PhyloP100		-3.0

Splicing

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

Other links and lift over

dbSNP: rs6457594; hg19: chr6-32443961;