rs12602288

Variant names:

• chr17-70577737-A-C
• rs12602288

Your query was ambiguous. Multiple possible variants found:

• chr17-70577737-A-C
• chr17-70577737-A-T

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 0.405 in 151,964 control chromosomes in the GnomAD database, including 13,779 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 0.40 (13779 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.240
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.517 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: 0.405 AC: 61520 AN: 151846 Hom.: 13776 Cov.: 31

Gnomad AFR AF: 0.232

Gnomad AMI AF: 0.645

Gnomad AMR AF: 0.390

Gnomad ASJ AF: 0.487

Gnomad EAS AF: 0.183

Gnomad SAS AF: 0.437

Gnomad FIN AF: 0.400

Gnomad MID AF: 0.443

Gnomad NFE AF: 0.521

Gnomad OTH AF: 0.432

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

GnomAD4 genome AF: 0.405 AC: 61533 AN: 151964 Hom.: 13779 Cov.: 31 AF XY: 0.397 AC XY: 29482 AN XY: 74270

African (AFR) AF: 0.232 AC: 9601 AN: 41470

American (AMR) AF: 0.390 AC: 5951 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.487 AC: 1689 AN: 3468

East Asian (EAS) AF: 0.182 AC: 936 AN: 5136

South Asian (SAS) AF: 0.437 AC: 2104 AN: 4814

European-Finnish (FIN) AF: 0.400 AC: 4219 AN: 10554

Middle Eastern (MID) AF: 0.432 AC: 127 AN: 294

European-Non Finnish (NFE) AF: 0.521 AC: 35406 AN: 67946

Other (OTH) AF: 0.432 AC: 912 AN: 2110

Alfa AF: 0.357 Hom.: 1427

Bravo AF: 0.395

Asia WGS AF: 0.332 AC: 1156 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	3.6
DANN	Benign	0.36
PhyloP100		0.24

Splicing

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

Other links and lift over

dbSNP: rs12602288; hg19: chr17-68573878;