rs13120644

Variant names:

• chr4-55732335-C-G
• rs13120644

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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;