rs12918335

Variant names:

• chr16-55212391-G-A
• rs12918335

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 0.11 in 152,148 control chromosomes in the GnomAD database, including 929 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 0.11 (929 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.781
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• 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: 0.110 AC: 16777 AN: 152030 Hom.: 926 Cov.: 32

Gnomad AFR AF: 0.0955

Gnomad AMI AF: 0.0143

Gnomad AMR AF: 0.0818

Gnomad ASJ AF: 0.114

Gnomad EAS AF: 0.0226

Gnomad SAS AF: 0.115

Gnomad FIN AF: 0.106

Gnomad MID AF: 0.104

Gnomad NFE AF: 0.134

Gnomad OTH AF: 0.110

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

GnomAD4 genome AF: 0.110 AC: 16781 AN: 152148 Hom.: 929 Cov.: 32 AF XY: 0.108 AC XY: 8054 AN XY: 74396

African (AFR) AF: 0.0957 AC: 3969 AN: 41490

American (AMR) AF: 0.0816 AC: 1248 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.114 AC: 397 AN: 3470

East Asian (EAS) AF: 0.0225 AC: 116 AN: 5160

South Asian (SAS) AF: 0.114 AC: 551 AN: 4820

European-Finnish (FIN) AF: 0.106 AC: 1127 AN: 10598

Middle Eastern (MID) AF: 0.102 AC: 30 AN: 294

European-Non Finnish (NFE) AF: 0.134 AC: 9103 AN: 68004

Other (OTH) AF: 0.107 AC: 227 AN: 2114

Alfa AF: 0.128 Hom.: 652

Bravo AF: 0.108

Asia WGS AF: 0.0600 AC: 207 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.79
DANN	Benign	0.49
PhyloP100		-0.78

Splicing

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

Other links and lift over

dbSNP: rs12918335; hg19: chr16-55246303;