rs4073360

Variant names:

• chr12-38481350-A-G
• rs4073360

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.643 in 151,750 control chromosomes in the GnomAD database, including 37,008 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 0.64 (37008 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.626

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.24).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.868 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: 0.644 AC: 97584 AN: 151632 Hom.: 37015 Cov.: 32

Gnomad AFR AF: 0.280

Gnomad AMI AF: 0.799

Gnomad AMR AF: 0.590

Gnomad ASJ AF: 0.749

Gnomad EAS AF: 0.196

Gnomad SAS AF: 0.554

Gnomad FIN AF: 0.862

Gnomad MID AF: 0.763

Gnomad NFE AF: 0.874

Gnomad OTH AF: 0.680

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

GnomAD4 genome AF: 0.643 AC: 97573 AN: 151750 Hom.: 37008 Cov.: 32 AF XY: 0.638 AC XY: 47269 AN XY: 74118

Gnomad4 AFR AF: 0.279

Gnomad4 AMR AF: 0.589

Gnomad4 ASJ AF: 0.749

Gnomad4 EAS AF: 0.196

Gnomad4 SAS AF: 0.555

Gnomad4 FIN AF: 0.862

Gnomad4 NFE AF: 0.874

Gnomad4 OTH AF: 0.672

Alfa AF: 0.714 Hom.: 6771

Bravo AF: 0.606

Asia WGS AF: 0.374 AC: 1302 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.24
CADD	Benign	17
DANN	Benign	0.92

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4073360; hg19: chr12-38875152;