rs4712032

Variant names:

• chr6-13553811-A-G
• rs4712032

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 0.31 in 152,196 control chromosomes in the GnomAD database, including 7,697 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 (7697 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.791
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.376 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.310 AC: 47165 AN: 152078 Hom.: 7684 Cov.: 33

Gnomad AFR AF: 0.211

Gnomad AMI AF: 0.641

Gnomad AMR AF: 0.384

Gnomad ASJ AF: 0.334

Gnomad EAS AF: 0.229

Gnomad SAS AF: 0.330

Gnomad FIN AF: 0.299

Gnomad MID AF: 0.313

Gnomad NFE AF: 0.354

Gnomad OTH AF: 0.345

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

GnomAD4 genome AF: 0.310 AC: 47214 AN: 152196 Hom.: 7697 Cov.: 33 AF XY: 0.308 AC XY: 22915 AN XY: 74418

African (AFR) AF: 0.211 AC: 8776 AN: 41510

American (AMR) AF: 0.384 AC: 5881 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.334 AC: 1158 AN: 3468

East Asian (EAS) AF: 0.230 AC: 1191 AN: 5178

South Asian (SAS) AF: 0.329 AC: 1592 AN: 4832

European-Finnish (FIN) AF: 0.299 AC: 3168 AN: 10592

Middle Eastern (MID) AF: 0.323 AC: 95 AN: 294

European-Non Finnish (NFE) AF: 0.354 AC: 24049 AN: 67998

Other (OTH) AF: 0.342 AC: 722 AN: 2114

Alfa AF: 0.348 Hom.: 19190

Bravo AF: 0.310

Asia WGS AF: 0.263 AC: 919 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	3.7
DANN	Benign	0.81
PhyloP100		0.79

Splicing

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

Other links and lift over

dbSNP: rs4712032; hg19: chr6-13554043;