rs12603122

Variant names:

• chr17-13201827-C-T
• rs12603122

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 0.148 in 152,012 control chromosomes in the GnomAD database, including 2,209 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 0.15 (2209 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.373
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.473 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: 0.148 AC: 22539 AN: 151894 Hom.: 2204 Cov.: 32

Gnomad AFR AF: 0.129

Gnomad AMI AF: 0.291

Gnomad AMR AF: 0.117

Gnomad ASJ AF: 0.137

Gnomad EAS AF: 0.488

Gnomad SAS AF: 0.360

Gnomad FIN AF: 0.110

Gnomad MID AF: 0.241

Gnomad NFE AF: 0.130

Gnomad OTH AF: 0.154

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

GnomAD4 genome AF: 0.148 AC: 22567 AN: 152012 Hom.: 2209 Cov.: 32 AF XY: 0.153 AC XY: 11394 AN XY: 74308

African (AFR) AF: 0.129 AC: 5366 AN: 41476

American (AMR) AF: 0.117 AC: 1785 AN: 15238

Ashkenazi Jewish (ASJ) AF: 0.137 AC: 477 AN: 3472

East Asian (EAS) AF: 0.489 AC: 2529 AN: 5172

South Asian (SAS) AF: 0.358 AC: 1722 AN: 4812

European-Finnish (FIN) AF: 0.110 AC: 1159 AN: 10558

Middle Eastern (MID) AF: 0.235 AC: 69 AN: 294

European-Non Finnish (NFE) AF: 0.130 AC: 8866 AN: 67974

Other (OTH) AF: 0.156 AC: 329 AN: 2106

Alfa AF: 0.142 Hom.: 7449

Bravo AF: 0.143

Asia WGS AF: 0.389 AC: 1351 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	3.5
DANN	Benign	0.66
PhyloP100		0.37

Splicing

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

Other links and lift over

dbSNP: rs12603122; hg19: chr17-13105144;