rs1024612

Variant names:

• chr17-34222337-A-G
• rs1024612

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;