chr4-43535583-T-G

Position:

• chr4-43535583-T-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 0.0486 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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;