rs2506933

chr6-92905732-T-C

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 0.211 in 151,830 control chromosomes in the GnomAD database, including 7,108 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 0.21 (7108 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0480

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.547 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: 0.210 AC: 31874 AN: 151712 Hom.: 7067 Cov.: 32

Gnomad AFR AF: 0.552

Gnomad AMI AF: 0.0296

Gnomad AMR AF: 0.231

Gnomad ASJ AF: 0.0922

Gnomad EAS AF: 0.139

Gnomad SAS AF: 0.0729

Gnomad FIN AF: 0.0406

Gnomad MID AF: 0.182

Gnomad NFE AF: 0.0486

Gnomad OTH AF: 0.180

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

GnomAD4 genome AF: 0.211 AC: 31973 AN: 151830 Hom.: 7108 Cov.: 32 AF XY: 0.209 AC XY: 15494 AN XY: 74218

Gnomad4 AFR AF: 0.553

Gnomad4 AMR AF: 0.232

Gnomad4 ASJ AF: 0.0922

Gnomad4 EAS AF: 0.139

Gnomad4 SAS AF: 0.0729

Gnomad4 FIN AF: 0.0406

Gnomad4 NFE AF: 0.0486

Gnomad4 OTH AF: 0.181

Alfa AF: 0.0784 Hom.: 1613

Bravo AF: 0.243

Asia WGS AF: 0.143 AC: 497 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
Cadd	Benign	9.3
Dann	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2506933; hg19: chr6-93615450;