chr6-467773-A-G

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

ENSG00000286364 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000286364	ENST00000661640.1	n.336-7435A>G		intron_variant	Intron 1 of 1

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

Gnomad4 AFR AF: 0.798

Gnomad4 AMR AF: 0.835

Gnomad4 ASJ AF: 0.887

Gnomad4 EAS AF: 0.817

Gnomad4 SAS AF: 0.797

Gnomad4 FIN AF: 0.892

Gnomad4 NFE AF: 0.909

Gnomad4 OTH AF: 0.864

Alfa AF: 0.894 Hom.: 78841

Bravo AF: 0.857

Asia WGS AF: 0.798 AC: 2775 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4959923; hg19: chr6-467773;