rs9405705

Variant names:

• chr6-470384-C-G
• rs9405705
• ENST00000661640.1:n.336-4824C>G

Your query was ambiguous. Multiple possible variants found:

• chr6-470384-C-G
• chr6-470384-C-T

Variant summary

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

The ENST00000661640.1(ENSG00000286364):​n.336-4824C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.721 in 152,098 control chromosomes in the GnomAD database, including 42,648 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 0.72 (42648 hom., cov: 32)
• Consequence: ENSG00000286364 ENST00000661640.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.305

Genes affected

ENSG00000286364 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.73).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.871 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.336-4824C>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.721 AC: 109615 AN: 151978 Hom.: 42635 Cov.: 32

Gnomad AFR AF: 0.414

Gnomad AMI AF: 0.931

Gnomad AMR AF: 0.731

Gnomad ASJ AF: 0.879

Gnomad EAS AF: 0.689

Gnomad SAS AF: 0.659

Gnomad FIN AF: 0.870

Gnomad MID AF: 0.791

Gnomad NFE AF: 0.877

Gnomad OTH AF: 0.750

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

GnomAD4 genome AF: 0.721 AC: 109665 AN: 152098 Hom.: 42648 Cov.: 32 AF XY: 0.718 AC XY: 53406 AN XY: 74352

Gnomad4 AFR AF: 0.414

Gnomad4 AMR AF: 0.730

Gnomad4 ASJ AF: 0.879

Gnomad4 EAS AF: 0.690

Gnomad4 SAS AF: 0.662

Gnomad4 FIN AF: 0.870

Gnomad4 NFE AF: 0.877

Gnomad4 OTH AF: 0.751

Alfa AF: 0.723 Hom.: 2566

Bravo AF: 0.700

Asia WGS AF: 0.628 AC: 2187 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.73
CADD	Benign	3.7
DANN	Benign	0.83

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9405705; hg19: chr6-470384;