rs176461

Positions:

• chr6-28858628-A-G

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 0.0556 in 152,242 control chromosomes in the GnomAD database, including 258 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 0.056 (258 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.941

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0755 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: 0.0556 AC: 8457 AN: 152124 Hom.: 257 Cov.: 32

Gnomad AFR AF: 0.0752

Gnomad AMI AF: 0.0231

Gnomad AMR AF: 0.0409

Gnomad ASJ AF: 0.0519

Gnomad EAS AF: 0.0196

Gnomad SAS AF: 0.0823

Gnomad FIN AF: 0.0420

Gnomad MID AF: 0.0759

Gnomad NFE AF: 0.0503

Gnomad OTH AF: 0.0621

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

GnomAD4 genome AF: 0.0556 AC: 8464 AN: 152242 Hom.: 258 Cov.: 32 AF XY: 0.0559 AC XY: 4158 AN XY: 74438

Gnomad4 AFR AF: 0.0752

Gnomad4 AMR AF: 0.0408

Gnomad4 ASJ AF: 0.0519

Gnomad4 EAS AF: 0.0197

Gnomad4 SAS AF: 0.0821

Gnomad4 FIN AF: 0.0420

Gnomad4 NFE AF: 0.0503

Gnomad4 OTH AF: 0.0615

Alfa AF: 0.0506 Hom.: 126

Bravo AF: 0.0563

Asia WGS AF: 0.0500 AC: 175 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	6.4
DANN	Benign	0.82

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs176461; hg19: chr6-28826405;