rs444903

Positions:

• chr12-59440679-A-C

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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

Gnomad4 AFR AF: 0.0558

Gnomad4 AMR AF: 0.146

Gnomad4 ASJ AF: 0.112

Gnomad4 EAS AF: 0.0601

Gnomad4 SAS AF: 0.0805

Gnomad4 FIN AF: 0.212

Gnomad4 NFE AF: 0.163

Gnomad4 OTH AF: 0.130

Alfa AF: 0.143 Hom.: 180

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs444903; hg19: chr12-59834460;