rs1264459

Variant names:

• chr6-30488143-G-A
• rs1264459

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 28 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.809 AC: 33568 AN: 41490

American (AMR) AF: 0.840 AC: 12833 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.867 AC: 3009 AN: 3470

East Asian (EAS) AF: 0.951 AC: 4936 AN: 5190

South Asian (SAS) AF: 0.921 AC: 4438 AN: 4818

European-Finnish (FIN) AF: 0.888 AC: 9407 AN: 10590

Middle Eastern (MID) AF: 0.833 AC: 245 AN: 294

European-Non Finnish (NFE) AF: 0.832 AC: 56618 AN: 68026

Other (OTH) AF: 0.826 AC: 1740 AN: 2106

Alfa AF: 0.837 Hom.: 170305

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
PhyloP100		-3.2

Splicing

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

Other links and lift over

dbSNP: rs1264459; hg19: chr6-30455920;