rs12418204

Variant names:

• chr11-72539079-G-A
• rs12418204

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 0.0591 in 152,156 control chromosomes in the GnomAD database, including 263 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 0.059 (263 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.700
• Publications: 9 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.74).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.07 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: 0.0591 AC: 8993 AN: 152038 Hom.: 263 Cov.: 30

Gnomad AFR AF: 0.0722

Gnomad AMI AF: 0.0274

Gnomad AMR AF: 0.0569

Gnomad ASJ AF: 0.0634

Gnomad EAS AF: 0.0703

Gnomad SAS AF: 0.0363

Gnomad FIN AF: 0.0393

Gnomad MID AF: 0.0222

Gnomad NFE AF: 0.0562

Gnomad OTH AF: 0.0526

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

GnomAD4 genome AF: 0.0591 AC: 8999 AN: 152156 Hom.: 263 Cov.: 30 AF XY: 0.0592 AC XY: 4401 AN XY: 74384

African (AFR) AF: 0.0722 AC: 2995 AN: 41494

American (AMR) AF: 0.0567 AC: 867 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.0634 AC: 220 AN: 3470

East Asian (EAS) AF: 0.0699 AC: 362 AN: 5180

South Asian (SAS) AF: 0.0363 AC: 175 AN: 4820

European-Finnish (FIN) AF: 0.0393 AC: 416 AN: 10588

Middle Eastern (MID) AF: 0.0272 AC: 8 AN: 294

European-Non Finnish (NFE) AF: 0.0562 AC: 3821 AN: 67998

Other (OTH) AF: 0.0521 AC: 110 AN: 2112

Alfa AF: 0.0581 Hom.: 879

Bravo AF: 0.0607

Asia WGS AF: 0.0690 AC: 238 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.74
CADD	Benign	4.2
DANN	Benign	0.78
PhyloP100		0.70

Splicing

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

Other links and lift over

dbSNP: rs12418204; hg19: chr11-72250123;