rs12511469

Variant names:

• chr4-154530607-T-A
• rs12511469

Your query was ambiguous. Multiple possible variants found:

• chr4-154530607-T-A
• chr4-154530607-T-C
• chr4-154530607-T-G

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 0.184 in 151,060 control chromosomes in the GnomAD database, including 3,287 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 (3287 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0660
• Publications: 11 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 (EAS) allele frequency at 95% confidence interval = 0.535 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: 0.184 AC: 27842 AN: 150952 Hom.: 3289 Cov.: 29

Gnomad AFR AF: 0.0792

Gnomad AMI AF: 0.316

Gnomad AMR AF: 0.214

Gnomad ASJ AF: 0.148

Gnomad EAS AF: 0.552

Gnomad SAS AF: 0.244

Gnomad FIN AF: 0.261

Gnomad MID AF: 0.158

Gnomad NFE AF: 0.198

Gnomad OTH AF: 0.179

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

GnomAD4 genome AF: 0.184 AC: 27841 AN: 151060 Hom.: 3287 Cov.: 29 AF XY: 0.191 AC XY: 14109 AN XY: 73688

African (AFR) AF: 0.0791 AC: 3265 AN: 41272

American (AMR) AF: 0.214 AC: 3239 AN: 15120

Ashkenazi Jewish (ASJ) AF: 0.148 AC: 513 AN: 3468

East Asian (EAS) AF: 0.552 AC: 2841 AN: 5148

South Asian (SAS) AF: 0.245 AC: 1168 AN: 4768

European-Finnish (FIN) AF: 0.261 AC: 2676 AN: 10256

Middle Eastern (MID) AF: 0.151 AC: 44 AN: 292

European-Non Finnish (NFE) AF: 0.198 AC: 13434 AN: 67734

Other (OTH) AF: 0.178 AC: 373 AN: 2092

Alfa AF: 0.206 Hom.: 2109

Bravo AF: 0.178

Asia WGS AF: 0.338 AC: 1174 AN: 3478

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	0.52
PhyloP100		-0.066

Splicing

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

Other links and lift over

dbSNP: rs12511469; hg19: chr4-155451759;