rs1264511

Variant names:

• chr6-30446195-G-C
• rs1264511

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 0.634 in 152,082 control chromosomes in the GnomAD database, including 30,756 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 0.63 (30756 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.78
• Publications: 13 publications found

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 (EAS) allele frequency at 95% confidence interval = 0.78 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: 0.634 AC: 96288 AN: 151964 Hom.: 30727 Cov.: 31

Gnomad AFR AF: 0.669

Gnomad AMI AF: 0.668

Gnomad AMR AF: 0.621

Gnomad ASJ AF: 0.692

Gnomad EAS AF: 0.801

Gnomad SAS AF: 0.718

Gnomad FIN AF: 0.631

Gnomad MID AF: 0.633

Gnomad NFE AF: 0.594

Gnomad OTH AF: 0.625

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

GnomAD4 genome AF: 0.634 AC: 96373 AN: 152082 Hom.: 30756 Cov.: 31 AF XY: 0.634 AC XY: 47100 AN XY: 74336

African (AFR) AF: 0.669 AC: 27737 AN: 41470

American (AMR) AF: 0.621 AC: 9501 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.692 AC: 2402 AN: 3470

East Asian (EAS) AF: 0.800 AC: 4142 AN: 5178

South Asian (SAS) AF: 0.718 AC: 3455 AN: 4814

European-Finnish (FIN) AF: 0.631 AC: 6656 AN: 10548

Middle Eastern (MID) AF: 0.616 AC: 181 AN: 294

European-Non Finnish (NFE) AF: 0.594 AC: 40361 AN: 67986

Other (OTH) AF: 0.629 AC: 1329 AN: 2112

Alfa AF: 0.611 Hom.: 3580

Bravo AF: 0.637

Asia WGS AF: 0.745 AC: 2587 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	0.70
DANN	Benign	0.26
PhyloP100		-1.8

Splicing

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

Other links and lift over

dbSNP: rs1264511; hg19: chr6-30413972;