rs4494364

Variant names:

• chr12-91083337-G-A
• rs4494364

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 0.166 in 151,890 control chromosomes in the GnomAD database, including 2,551 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 0.17 (2551 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.659
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.279 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: 0.166 AC: 25259 AN: 151772 Hom.: 2546 Cov.: 32

Gnomad AFR AF: 0.283

Gnomad AMI AF: 0.0592

Gnomad AMR AF: 0.137

Gnomad ASJ AF: 0.193

Gnomad EAS AF: 0.0558

Gnomad SAS AF: 0.0560

Gnomad FIN AF: 0.0865

Gnomad MID AF: 0.187

Gnomad NFE AF: 0.131

Gnomad OTH AF: 0.160

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

GnomAD4 genome AF: 0.166 AC: 25286 AN: 151890 Hom.: 2551 Cov.: 32 AF XY: 0.160 AC XY: 11915 AN XY: 74258

African (AFR) AF: 0.283 AC: 11713 AN: 41410

American (AMR) AF: 0.136 AC: 2077 AN: 15240

Ashkenazi Jewish (ASJ) AF: 0.193 AC: 671 AN: 3472

East Asian (EAS) AF: 0.0557 AC: 288 AN: 5170

South Asian (SAS) AF: 0.0561 AC: 270 AN: 4816

European-Finnish (FIN) AF: 0.0865 AC: 912 AN: 10542

Middle Eastern (MID) AF: 0.188 AC: 54 AN: 288

European-Non Finnish (NFE) AF: 0.131 AC: 8903 AN: 67924

Other (OTH) AF: 0.163 AC: 344 AN: 2116

Alfa AF: 0.166 Hom.: 365

Bravo AF: 0.177

Asia WGS AF: 0.0660 AC: 228 AN: 3458

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.59
DANN	Benign	0.51
PhyloP100		-0.66

Splicing

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

Other links and lift over

dbSNP: rs4494364; hg19: chr12-91477114;