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. The variant received -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
• Publications: 33 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.929 AC: 38587 AN: 41550

American (AMR) AF: 0.856 AC: 13096 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.829 AC: 2877 AN: 3472

East Asian (EAS) AF: 0.919 AC: 4762 AN: 5180

South Asian (SAS) AF: 0.916 AC: 4422 AN: 4830

European-Finnish (FIN) AF: 0.835 AC: 8854 AN: 10598

Middle Eastern (MID) AF: 0.782 AC: 230 AN: 294

European-Non Finnish (NFE) AF: 0.799 AC: 54342 AN: 68010

Other (OTH) AF: 0.822 AC: 1733 AN: 2108

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
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs1024610; hg19: chr17-32580231;