rs209130

Positions:

• chr6-28900023-C-T

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 0.61 in 152,024 control chromosomes in the GnomAD database, including 30,576 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 0.61 (30576 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.447

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.863 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.610 AC: 92602 AN: 151906 Hom.: 30516 Cov.: 32

Gnomad AFR AF: 0.871

Gnomad AMI AF: 0.578

Gnomad AMR AF: 0.580

Gnomad ASJ AF: 0.553

Gnomad EAS AF: 0.656

Gnomad SAS AF: 0.578

Gnomad FIN AF: 0.404

Gnomad MID AF: 0.522

Gnomad NFE AF: 0.491

Gnomad OTH AF: 0.614

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

GnomAD4 genome AF: 0.610 AC: 92710 AN: 152024 Hom.: 30576 Cov.: 32 AF XY: 0.605 AC XY: 44966 AN XY: 74272

Gnomad4 AFR AF: 0.871

Gnomad4 AMR AF: 0.579

Gnomad4 ASJ AF: 0.553

Gnomad4 EAS AF: 0.657

Gnomad4 SAS AF: 0.579

Gnomad4 FIN AF: 0.404

Gnomad4 NFE AF: 0.491

Gnomad4 OTH AF: 0.607

Alfa AF: 0.515 Hom.: 10856

Bravo AF: 0.640

Asia WGS AF: 0.570 AC: 1982 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.2
DANN	Benign	0.39

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs209130; hg19: chr6-28867800;