ENST00000661640.1:n.336-7435A>G

Variant names:

• chr6-467773-A-G
• rs4959923
• ENST00000661640.1:n.336-7435A>G

Variant summary

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

The ENST00000661640.1(ENSG00000286364):​n.336-7435A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.863 in 152,116 control chromosomes in the GnomAD database, including 56,842 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 (56842 hom., cov: 31)
• Consequence: ENSG00000286364 ENST00000661640.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.00
• Publications: 6 publications found

Genes affected

ENSG00000286364 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.903 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000661640.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000286364	ENST00000661640.1		n.336-7435A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.863 AC: 131149 AN: 151998 Hom.: 56808 Cov.: 31

Gnomad AFR AF: 0.798

Gnomad AMI AF: 0.971

Gnomad AMR AF: 0.835

Gnomad ASJ AF: 0.887

Gnomad EAS AF: 0.818

Gnomad SAS AF: 0.795

Gnomad FIN AF: 0.892

Gnomad MID AF: 0.899

Gnomad NFE AF: 0.909

Gnomad OTH AF: 0.863

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

GnomAD4 genome AF: 0.863 AC: 131242 AN: 152116 Hom.: 56842 Cov.: 31 AF XY: 0.860 AC XY: 63935 AN XY: 74360

African (AFR) AF: 0.798 AC: 33104 AN: 41484

American (AMR) AF: 0.835 AC: 12768 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.887 AC: 3080 AN: 3472

East Asian (EAS) AF: 0.817 AC: 4200 AN: 5138

South Asian (SAS) AF: 0.797 AC: 3836 AN: 4812

European-Finnish (FIN) AF: 0.892 AC: 9442 AN: 10588

Middle Eastern (MID) AF: 0.898 AC: 264 AN: 294

European-Non Finnish (NFE) AF: 0.909 AC: 61834 AN: 68012

Other (OTH) AF: 0.864 AC: 1828 AN: 2116

Alfa AF: 0.890 Hom.: 99961

Bravo AF: 0.857

Asia WGS AF: 0.798 AC: 2775 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.17
DANN	Benign	0.21
PhyloP100		-2.0

Splicing

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

Other links and lift over

dbSNP: rs4959923; hg19: chr6-467773;