rs2506933

Variant names:

• chr6-92905732-T-C
• rs2506933

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 6 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.553 AC: 22866 AN: 41376

American (AMR) AF: 0.232 AC: 3529 AN: 15202

Ashkenazi Jewish (ASJ) AF: 0.0922 AC: 319 AN: 3460

East Asian (EAS) AF: 0.139 AC: 715 AN: 5144

South Asian (SAS) AF: 0.0729 AC: 352 AN: 4826

European-Finnish (FIN) AF: 0.0406 AC: 431 AN: 10614

Middle Eastern (MID) AF: 0.185 AC: 54 AN: 292

European-Non Finnish (NFE) AF: 0.0486 AC: 3298 AN: 67896

Other (OTH) AF: 0.181 AC: 382 AN: 2108

Alfa AF: 0.102 Hom.: 3946

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
PhyloP100		0.048

Splicing

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

Other links and lift over

dbSNP: rs2506933; hg19: chr6-93615450;