rs1024610

chr17-34253212-T-Achr17-34253212-T-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 0.85 in 152,248 control chromosomes in the GnomAD database, including 55,235 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 0.85 (55235 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.04

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.921 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: 0.849 AC: 129232 AN: 152130 Hom.: 55172 Cov.: 33

Gnomad AFR AF: 0.929

Gnomad AMI AF: 0.498

Gnomad AMR AF: 0.856

Gnomad ASJ AF: 0.829

Gnomad EAS AF: 0.919

Gnomad SAS AF: 0.916

Gnomad FIN AF: 0.835

Gnomad MID AF: 0.778

Gnomad NFE AF: 0.799

Gnomad OTH AF: 0.822

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

GnomAD4 genome AF: 0.850 AC: 129357 AN: 152248 Hom.: 55235 Cov.: 33 AF XY: 0.853 AC XY: 63530 AN XY: 74438

Gnomad4 AFR AF: 0.929

Gnomad4 AMR AF: 0.856

Gnomad4 ASJ AF: 0.829

Gnomad4 EAS AF: 0.919

Gnomad4 SAS AF: 0.916

Gnomad4 FIN AF: 0.835

Gnomad4 NFE AF: 0.799

Gnomad4 OTH AF: 0.822

Alfa AF: 0.805 Hom.: 2841

Bravo AF: 0.852

Asia WGS AF: 0.923 AC: 3211 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
Cadd	Benign	0.044
Dann	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1024610; hg19: chr17-32580231;