rs6925476

chr6-46183494-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 0.232 in 152,124 control chromosomes in the GnomAD database, including 4,239 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 0.23 (4239 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.60

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.245 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: 0.232 AC: 35274 AN: 152006 Hom.: 4236 Cov.: 32

Gnomad AFR AF: 0.246

Gnomad AMI AF: 0.169

Gnomad AMR AF: 0.198

Gnomad ASJ AF: 0.219

Gnomad EAS AF: 0.131

Gnomad SAS AF: 0.194

Gnomad FIN AF: 0.200

Gnomad MID AF: 0.168

Gnomad NFE AF: 0.248

Gnomad OTH AF: 0.239

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

GnomAD4 genome AF: 0.232 AC: 35294 AN: 152124 Hom.: 4239 Cov.: 32 AF XY: 0.227 AC XY: 16885 AN XY: 74336

Gnomad4 AFR AF: 0.246

Gnomad4 AMR AF: 0.198

Gnomad4 ASJ AF: 0.219

Gnomad4 EAS AF: 0.131

Gnomad4 SAS AF: 0.194

Gnomad4 FIN AF: 0.200

Gnomad4 NFE AF: 0.248

Gnomad4 OTH AF: 0.235

Alfa AF: 0.242 Hom.: 9392

Bravo AF: 0.232

Asia WGS AF: 0.176 AC: 614 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	0.067
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: rs6925476; hg19: chr6-46151231;