chr4-33746904-A-C

Position:

• chr4-33746904-A-C

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 0.203 in 152,138 control chromosomes in the GnomAD database, including 4,555 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 0.20 (4555 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0110

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 (AFR) allele frequency at 95% confidence interval = 0.394 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: 0.202 AC: 30771 AN: 152020 Hom.: 4543 Cov.: 33

Gnomad AFR AF: 0.399

Gnomad AMI AF: 0.0373

Gnomad AMR AF: 0.211

Gnomad ASJ AF: 0.138

Gnomad EAS AF: 0.320

Gnomad SAS AF: 0.156

Gnomad FIN AF: 0.115

Gnomad MID AF: 0.139

Gnomad NFE AF: 0.0953

Gnomad OTH AF: 0.182

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

GnomAD4 genome AF: 0.203 AC: 30815 AN: 152138 Hom.: 4555 Cov.: 33 AF XY: 0.205 AC XY: 15277 AN XY: 74368

Gnomad4 AFR AF: 0.399

Gnomad4 AMR AF: 0.211

Gnomad4 ASJ AF: 0.138

Gnomad4 EAS AF: 0.319

Gnomad4 SAS AF: 0.156

Gnomad4 FIN AF: 0.115

Gnomad4 NFE AF: 0.0954

Gnomad4 OTH AF: 0.181

Alfa AF: 0.181 Hom.: 682

Bravo AF: 0.216

Asia WGS AF: 0.289 AC: 1005 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	2.2
DANN	Benign	0.38

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1373494; hg19: chr4-33748526;