rs444903

Variant names:

• chr12-59440679-A-C
• rs444903

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 0.128 in 151,998 control chromosomes in the GnomAD database, including 1,479 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 0.13 (1479 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.240
• Publications: 11 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 (NFE) allele frequency at 95% confidence interval = 0.16 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: 0.128 AC: 19387 AN: 151882 Hom.: 1478 Cov.: 32

Gnomad AFR AF: 0.0559

Gnomad AMI AF: 0.163

Gnomad AMR AF: 0.146

Gnomad ASJ AF: 0.112

Gnomad EAS AF: 0.0600

Gnomad SAS AF: 0.0806

Gnomad FIN AF: 0.212

Gnomad MID AF: 0.120

Gnomad NFE AF: 0.163

Gnomad OTH AF: 0.131

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

GnomAD4 genome AF: 0.128 AC: 19390 AN: 151998 Hom.: 1479 Cov.: 32 AF XY: 0.127 AC XY: 9412 AN XY: 74274

African (AFR) AF: 0.0558 AC: 2316 AN: 41482

American (AMR) AF: 0.146 AC: 2233 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.112 AC: 388 AN: 3470

East Asian (EAS) AF: 0.0601 AC: 309 AN: 5140

South Asian (SAS) AF: 0.0805 AC: 387 AN: 4810

European-Finnish (FIN) AF: 0.212 AC: 2239 AN: 10558

Middle Eastern (MID) AF: 0.126 AC: 37 AN: 294

European-Non Finnish (NFE) AF: 0.163 AC: 11058 AN: 67960

Other (OTH) AF: 0.130 AC: 274 AN: 2110

Alfa AF: 0.140 Hom.: 181

Bravo AF: 0.122

Asia WGS AF: 0.0620 AC: 217 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	7.1
DANN	Benign	0.73
PhyloP100		0.24

Splicing

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

Other links and lift over

dbSNP: rs444903; hg19: chr12-59834460;