rs4073360

Positions:

• chr12-38481350-A-G

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: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.626

Genes affected

(HGNC:):

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/exons	MANE	Protein	UniProt
		n.38481350A>G		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;