rs13120644

Positions:

• chr4-55732335-C-G

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 0.415 in 151,910 control chromosomes in the GnomAD database, including 14,465 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 0.42 (14465 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.90

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.878 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: 0.415 AC: 62994 AN: 151792 Hom.: 14445 Cov.: 32

Gnomad AFR AF: 0.282

Gnomad AMI AF: 0.259

Gnomad AMR AF: 0.506

Gnomad ASJ AF: 0.532

Gnomad EAS AF: 0.898

Gnomad SAS AF: 0.658

Gnomad FIN AF: 0.388

Gnomad MID AF: 0.497

Gnomad NFE AF: 0.421

Gnomad OTH AF: 0.438

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

GnomAD4 genome AF: 0.415 AC: 63051 AN: 151910 Hom.: 14465 Cov.: 32 AF XY: 0.422 AC XY: 31299 AN XY: 74248

Gnomad4 AFR AF: 0.282

Gnomad4 AMR AF: 0.507

Gnomad4 ASJ AF: 0.532

Gnomad4 EAS AF: 0.899

Gnomad4 SAS AF: 0.659

Gnomad4 FIN AF: 0.388

Gnomad4 NFE AF: 0.421

Gnomad4 OTH AF: 0.443

Alfa AF: 0.420 Hom.: 1746

Bravo AF: 0.415

Asia WGS AF: 0.763 AC: 2653 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.30
DANN	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13120644; hg19: chr4-56598502;