rs17476793

Positions:

• chr6-30443211-G-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 0.0593 in 152,256 control chromosomes in the GnomAD database, including 308 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 0.059 (308 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.653

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.105 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: 0.0594 AC: 9035 AN: 152138 Hom.: 308 Cov.: 33

Gnomad AFR AF: 0.0460

Gnomad AMI AF: 0.0912

Gnomad AMR AF: 0.0469

Gnomad ASJ AF: 0.107

Gnomad EAS AF: 0.0310

Gnomad SAS AF: 0.113

Gnomad FIN AF: 0.0307

Gnomad MID AF: 0.117

Gnomad NFE AF: 0.0696

Gnomad OTH AF: 0.0733

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

GnomAD4 genome AF: 0.0593 AC: 9031 AN: 152256 Hom.: 308 Cov.: 33 AF XY: 0.0592 AC XY: 4408 AN XY: 74430

Gnomad4 AFR AF: 0.0459

Gnomad4 AMR AF: 0.0469

Gnomad4 ASJ AF: 0.107

Gnomad4 EAS AF: 0.0311

Gnomad4 SAS AF: 0.113

Gnomad4 FIN AF: 0.0307

Gnomad4 NFE AF: 0.0696

Gnomad4 OTH AF: 0.0725

Alfa AF: 0.0586 Hom.: 39

Bravo AF: 0.0585

Asia WGS AF: 0.0620 AC: 219 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.5
DANN	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17476793; hg19: chr6-30410988;