rs1264459

chr6-30488143-G-A

Variant summary

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

The variant allele was found at a frequency of 0.839 in 152,180 control chromosomes in the GnomAD database, including 53,637 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 0.84 (53637 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.17

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.929 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.839 AC: 127534 AN: 152062 Hom.: 53596 Cov.: 32

Gnomad AFR AF: 0.809

Gnomad AMI AF: 0.913

Gnomad AMR AF: 0.839

Gnomad ASJ AF: 0.867

Gnomad EAS AF: 0.951

Gnomad SAS AF: 0.921

Gnomad FIN AF: 0.888

Gnomad MID AF: 0.835

Gnomad NFE AF: 0.832

Gnomad OTH AF: 0.824

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

GnomAD4 genome AF: 0.839 AC: 127627 AN: 152180 Hom.: 53637 Cov.: 32 AF XY: 0.840 AC XY: 62487 AN XY: 74394

Gnomad4 AFR AF: 0.809

Gnomad4 AMR AF: 0.840

Gnomad4 ASJ AF: 0.867

Gnomad4 EAS AF: 0.951

Gnomad4 SAS AF: 0.921

Gnomad4 FIN AF: 0.888

Gnomad4 NFE AF: 0.832

Gnomad4 OTH AF: 0.826

Alfa AF: 0.837 Hom.: 55659

Bravo AF: 0.834

Asia WGS AF: 0.922 AC: 3209 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	0.15
Dann	Benign	0.94

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1264459; hg19: chr6-30455920;