1-53471504-A-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 0.392 in 152,056 control chromosomes in the GnomAD database, including 14,395 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 0.39 (14395 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -5.28

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.678 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.391 AC: 59464 AN: 151938 Hom.: 14360 Cov.: 33

Gnomad AFR AF: 0.684

Gnomad AMI AF: 0.120

Gnomad AMR AF: 0.254

Gnomad ASJ AF: 0.271

Gnomad EAS AF: 0.518

Gnomad SAS AF: 0.392

Gnomad FIN AF: 0.241

Gnomad MID AF: 0.310

Gnomad NFE AF: 0.269

Gnomad OTH AF: 0.364

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

GnomAD4 genome AF: 0.392 AC: 59554 AN: 152056 Hom.: 14395 Cov.: 33 AF XY: 0.388 AC XY: 28837 AN XY: 74306

Gnomad4 AFR AF: 0.684

Gnomad4 AMR AF: 0.253

Gnomad4 ASJ AF: 0.271

Gnomad4 EAS AF: 0.518

Gnomad4 SAS AF: 0.392

Gnomad4 FIN AF: 0.241

Gnomad4 NFE AF: 0.269

Gnomad4 OTH AF: 0.364

Alfa AF: 0.282 Hom.: 3337

Bravo AF: 0.405

Asia WGS AF: 0.462 AC: 1607 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
Cadd	Benign	0.0030
Dann	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1296438; hg19: chr1-53937177;