rs1286005

Variant names:

• chr6-7046219-T-C
• rs1286005

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 0.507 in 151,798 control chromosomes in the GnomAD database, including 22,390 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 0.51 (22390 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.979

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.658 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: 0.507 AC: 76963 AN: 151680 Hom.: 22387 Cov.: 30

Gnomad AFR AF: 0.272

Gnomad AMI AF: 0.722

Gnomad AMR AF: 0.526

Gnomad ASJ AF: 0.619

Gnomad EAS AF: 0.0670

Gnomad SAS AF: 0.344

Gnomad FIN AF: 0.623

Gnomad MID AF: 0.627

Gnomad NFE AF: 0.663

Gnomad OTH AF: 0.559

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

GnomAD4 genome AF: 0.507 AC: 76993 AN: 151798 Hom.: 22390 Cov.: 30 AF XY: 0.502 AC XY: 37265 AN XY: 74162

Gnomad4 AFR AF: 0.272

Gnomad4 AMR AF: 0.526

Gnomad4 ASJ AF: 0.619

Gnomad4 EAS AF: 0.0677

Gnomad4 SAS AF: 0.346

Gnomad4 FIN AF: 0.623

Gnomad4 NFE AF: 0.663

Gnomad4 OTH AF: 0.552

Alfa AF: 0.624 Hom.: 39907

Bravo AF: 0.488

Asia WGS AF: 0.212 AC: 740 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	6.7
DANN	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1286005; hg19: chr6-7046452;