rs1024610

Variant names:

• chr17-34253212-T-A
• rs1024610

Your query was ambiguous. Multiple possible variants found:

• chr17-34253212-T-A
• chr17-34253212-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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;