rs17476793

Variant names:

• chr6-30443211-G-C
• rs17476793

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 0.0593 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
• Publications: 12 publications found

ACMG classification

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

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.0459 AC: 1907 AN: 41550

American (AMR) AF: 0.0469 AC: 717 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.107 AC: 370 AN: 3466

East Asian (EAS) AF: 0.0311 AC: 161 AN: 5180

South Asian (SAS) AF: 0.113 AC: 544 AN: 4822

European-Finnish (FIN) AF: 0.0307 AC: 326 AN: 10602

Middle Eastern (MID) AF: 0.116 AC: 34 AN: 294

European-Non Finnish (NFE) AF: 0.0696 AC: 4736 AN: 68022

Other (OTH) AF: 0.0725 AC: 153 AN: 2110

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
PhyloP100		-0.65

Splicing

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

Other links and lift over

dbSNP: rs17476793; hg19: chr6-30410988;