rs2179915

Positions:

• chr6-33097957-C-A

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 0.132 in 151,810 control chromosomes in the GnomAD database, including 2,544 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 0.13 (2544 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.187

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.332 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: 0.132 AC: 20039 AN: 151694 Hom.: 2539 Cov.: 31

Gnomad AFR AF: 0.337

Gnomad AMI AF: 0.0417

Gnomad AMR AF: 0.0687

Gnomad ASJ AF: 0.0130

Gnomad EAS AF: 0.0129

Gnomad SAS AF: 0.0667

Gnomad FIN AF: 0.0510

Gnomad MID AF: 0.00949

Gnomad NFE AF: 0.0563

Gnomad OTH AF: 0.120

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

GnomAD4 genome AF: 0.132 AC: 20062 AN: 151810 Hom.: 2544 Cov.: 31 AF XY: 0.128 AC XY: 9489 AN XY: 74200

Gnomad4 AFR AF: 0.337

Gnomad4 AMR AF: 0.0686

Gnomad4 ASJ AF: 0.0130

Gnomad4 EAS AF: 0.0127

Gnomad4 SAS AF: 0.0664

Gnomad4 FIN AF: 0.0510

Gnomad4 NFE AF: 0.0563

Gnomad4 OTH AF: 0.118

Alfa AF: 0.0746 Hom.: 520

Bravo AF: 0.141

Asia WGS AF: 0.0880 AC: 307 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	2.8
DANN	Benign	0.14

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2179915; hg19: chr6-33065734;