rs12603538

Variant names:

• chr17-75301986-G-A
• rs12603538

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 0.185 in 152,110 control chromosomes in the GnomAD database, including 2,781 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 0.18 (2781 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0120
• Publications: 10 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.244 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: 0.185 AC: 28086 AN: 151992 Hom.: 2763 Cov.: 31

Gnomad AFR AF: 0.159

Gnomad AMI AF: 0.0967

Gnomad AMR AF: 0.154

Gnomad ASJ AF: 0.302

Gnomad EAS AF: 0.0429

Gnomad SAS AF: 0.253

Gnomad FIN AF: 0.177

Gnomad MID AF: 0.287

Gnomad NFE AF: 0.209

Gnomad OTH AF: 0.211

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

GnomAD4 genome AF: 0.185 AC: 28133 AN: 152110 Hom.: 2781 Cov.: 31 AF XY: 0.184 AC XY: 13717 AN XY: 74366

African (AFR) AF: 0.159 AC: 6597 AN: 41474

American (AMR) AF: 0.153 AC: 2342 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.302 AC: 1048 AN: 3470

East Asian (EAS) AF: 0.0426 AC: 221 AN: 5184

South Asian (SAS) AF: 0.256 AC: 1236 AN: 4828

European-Finnish (FIN) AF: 0.177 AC: 1873 AN: 10586

Middle Eastern (MID) AF: 0.288 AC: 84 AN: 292

European-Non Finnish (NFE) AF: 0.209 AC: 14195 AN: 67988

Other (OTH) AF: 0.213 AC: 449 AN: 2110

Alfa AF: 0.194 Hom.: 1392

Bravo AF: 0.179

Asia WGS AF: 0.194 AC: 675 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.91
DANN	Benign	0.46
PhyloP100		-0.012

Splicing

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

Other links and lift over

dbSNP: rs12603538; hg19: chr17-73298067;