rs1603218

Variant names:

• chr12-80748003-A-G
• rs1603218

Your query was ambiguous. Multiple possible variants found:

• chr12-80748003-A-G
• chr12-80748003-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 0.2 in 152,234 control chromosomes in the GnomAD database, including 3,772 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 0.20 (3772 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0420
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.33 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: 0.200 AC: 30421 AN: 152116 Hom.: 3764 Cov.: 32

Gnomad AFR AF: 0.0504

Gnomad AMI AF: 0.208

Gnomad AMR AF: 0.337

Gnomad ASJ AF: 0.287

Gnomad EAS AF: 0.177

Gnomad SAS AF: 0.272

Gnomad FIN AF: 0.259

Gnomad MID AF: 0.261

Gnomad NFE AF: 0.242

Gnomad OTH AF: 0.228

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

GnomAD4 genome AF: 0.200 AC: 30433 AN: 152234 Hom.: 3772 Cov.: 32 AF XY: 0.205 AC XY: 15266 AN XY: 74436

African (AFR) AF: 0.0503 AC: 2092 AN: 41560

American (AMR) AF: 0.337 AC: 5159 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.287 AC: 994 AN: 3466

East Asian (EAS) AF: 0.177 AC: 918 AN: 5184

South Asian (SAS) AF: 0.272 AC: 1310 AN: 4820

European-Finnish (FIN) AF: 0.259 AC: 2742 AN: 10590

Middle Eastern (MID) AF: 0.264 AC: 77 AN: 292

European-Non Finnish (NFE) AF: 0.242 AC: 16471 AN: 68008

Other (OTH) AF: 0.227 AC: 480 AN: 2114

Alfa AF: 0.223 Hom.: 2373

Bravo AF: 0.199

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.7
DANN	Benign	0.41
PhyloP100		0.042

Splicing

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

Other links and lift over

dbSNP: rs1603218; hg19: chr12-81141782; COSMIC: COSV107990529;