rs3858655

Variant names:

• chr12-96486464-C-A
• rs3858655

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 0.0901 in 151,934 control chromosomes in the GnomAD database, including 797 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 0.090 (797 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.322
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.132 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: 0.0902 AC: 13691 AN: 151816 Hom.: 797 Cov.: 30

Gnomad AFR AF: 0.0403

Gnomad AMI AF: 0.239

Gnomad AMR AF: 0.0826

Gnomad ASJ AF: 0.120

Gnomad EAS AF: 0.000770

Gnomad SAS AF: 0.0361

Gnomad FIN AF: 0.0532

Gnomad MID AF: 0.120

Gnomad NFE AF: 0.135

Gnomad OTH AF: 0.102

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

GnomAD4 genome AF: 0.0901 AC: 13690 AN: 151934 Hom.: 797 Cov.: 30 AF XY: 0.0847 AC XY: 6285 AN XY: 74240

African (AFR) AF: 0.0402 AC: 1666 AN: 41454

American (AMR) AF: 0.0824 AC: 1256 AN: 15240

Ashkenazi Jewish (ASJ) AF: 0.120 AC: 415 AN: 3472

East Asian (EAS) AF: 0.000772 AC: 4 AN: 5182

South Asian (SAS) AF: 0.0359 AC: 173 AN: 4816

European-Finnish (FIN) AF: 0.0532 AC: 560 AN: 10536

Middle Eastern (MID) AF: 0.122 AC: 36 AN: 294

European-Non Finnish (NFE) AF: 0.135 AC: 9150 AN: 67924

Other (OTH) AF: 0.101 AC: 212 AN: 2104

Alfa AF: 0.124 Hom.: 1896

Bravo AF: 0.0912

Asia WGS AF: 0.0250 AC: 87 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	1.5
DANN	Benign	0.32
PhyloP100		-0.32

Splicing

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

Other links and lift over

dbSNP: rs3858655; hg19: chr12-96880242;