chr4-43535583-T-G

Variant names:

• chr4-43535583-T-G
• rs13130255

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 0.0486 in 152,174 control chromosomes in the GnomAD database, including 264 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 0.049 (264 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.00

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0766 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: 0.0486 AC: 7396 AN: 152056 Hom.: 264 Cov.: 33

Gnomad AFR AF: 0.0138

Gnomad AMI AF: 0.0450

Gnomad AMR AF: 0.0272

Gnomad ASJ AF: 0.0609

Gnomad EAS AF: 0.000385

Gnomad SAS AF: 0.00911

Gnomad FIN AF: 0.0659

Gnomad MID AF: 0.0380

Gnomad NFE AF: 0.0784

Gnomad OTH AF: 0.0354

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

GnomAD4 genome AF: 0.0486 AC: 7395 AN: 152174 Hom.: 264 Cov.: 33 AF XY: 0.0464 AC XY: 3451 AN XY: 74390

Gnomad4 AFR AF: 0.0137

Gnomad4 AMR AF: 0.0272

Gnomad4 ASJ AF: 0.0609

Gnomad4 EAS AF: 0.000386

Gnomad4 SAS AF: 0.00932

Gnomad4 FIN AF: 0.0659

Gnomad4 NFE AF: 0.0784

Gnomad4 OTH AF: 0.0350

Alfa AF: 0.0676 Hom.: 534

Bravo AF: 0.0448

Asia WGS AF: 0.00404 AC: 14 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	0.098
DANN	Benign	0.80

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13130255; hg19: chr4-43537600;