rs12577147

Variant names:

• chr11-119347938-G-A
• rs12577147

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 0.309 in 152,080 control chromosomes in the GnomAD database, including 7,505 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 0.31 (7505 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.47
• Publications: 6 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 = 0.359 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: 0.309 AC: 46978 AN: 151962 Hom.: 7503 Cov.: 32

Gnomad AFR AF: 0.271

Gnomad AMI AF: 0.493

Gnomad AMR AF: 0.256

Gnomad ASJ AF: 0.316

Gnomad EAS AF: 0.373

Gnomad SAS AF: 0.209

Gnomad FIN AF: 0.344

Gnomad MID AF: 0.411

Gnomad NFE AF: 0.337

Gnomad OTH AF: 0.336

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

GnomAD4 genome AF: 0.309 AC: 46985 AN: 152080 Hom.: 7505 Cov.: 32 AF XY: 0.307 AC XY: 22852 AN XY: 74336

African (AFR) AF: 0.271 AC: 11251 AN: 41490

American (AMR) AF: 0.256 AC: 3905 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.316 AC: 1095 AN: 3470

East Asian (EAS) AF: 0.373 AC: 1928 AN: 5168

South Asian (SAS) AF: 0.209 AC: 1008 AN: 4826

European-Finnish (FIN) AF: 0.344 AC: 3640 AN: 10572

Middle Eastern (MID) AF: 0.408 AC: 120 AN: 294

European-Non Finnish (NFE) AF: 0.337 AC: 22882 AN: 67954

Other (OTH) AF: 0.334 AC: 706 AN: 2112

Alfa AF: 0.325 Hom.: 18451

Bravo AF: 0.305

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.97
DANN	Benign	0.75
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs12577147; hg19: chr11-119218648;