rs2179915

Variant names:

• chr6-33097957-C-A
• rs2179915

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;