rs1024612

chr17-34222337-A-G

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 0.617 in 152,072 control chromosomes in the GnomAD database, including 29,466 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 0.62 (29466 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.144

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.838 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: 0.617 AC: 93827 AN: 151954 Hom.: 29442 Cov.: 32

Gnomad AFR AF: 0.573

Gnomad AMI AF: 0.514

Gnomad AMR AF: 0.716

Gnomad ASJ AF: 0.610

Gnomad EAS AF: 0.859

Gnomad SAS AF: 0.817

Gnomad FIN AF: 0.630

Gnomad MID AF: 0.656

Gnomad NFE AF: 0.589

Gnomad OTH AF: 0.627

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

GnomAD4 genome AF: 0.617 AC: 93899 AN: 152072 Hom.: 29466 Cov.: 32 AF XY: 0.628 AC XY: 46696 AN XY: 74316

Gnomad4 AFR AF: 0.573

Gnomad4 AMR AF: 0.717

Gnomad4 ASJ AF: 0.610

Gnomad4 EAS AF: 0.859

Gnomad4 SAS AF: 0.817

Gnomad4 FIN AF: 0.630

Gnomad4 NFE AF: 0.589

Gnomad4 OTH AF: 0.630

Alfa AF: 0.610 Hom.: 5337

Bravo AF: 0.618

Asia WGS AF: 0.824 AC: 2863 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	1.2
Dann	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1024612; hg19: chr17-32549356;