rs243757

chr6-54521183-G-A

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 0.1 in 152,130 control chromosomes in the GnomAD database, including 1,269 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 0.10 (1269 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.23

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.228 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: 0.0999 AC: 15192 AN: 152012 Hom.: 1269 Cov.: 32

Gnomad AFR AF: 0.233

Gnomad AMI AF: 0.0307

Gnomad AMR AF: 0.0604

Gnomad ASJ AF: 0.0510

Gnomad EAS AF: 0.0143

Gnomad SAS AF: 0.0147

Gnomad FIN AF: 0.0256

Gnomad MID AF: 0.104

Gnomad NFE AF: 0.0562

Gnomad OTH AF: 0.0852

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

GnomAD4 genome AF: 0.100 AC: 15208 AN: 152130 Hom.: 1269 Cov.: 32 AF XY: 0.0950 AC XY: 7064 AN XY: 74380

Gnomad4 AFR AF: 0.232

Gnomad4 AMR AF: 0.0602

Gnomad4 ASJ AF: 0.0510

Gnomad4 EAS AF: 0.0143

Gnomad4 SAS AF: 0.0143

Gnomad4 FIN AF: 0.0256

Gnomad4 NFE AF: 0.0562

Gnomad4 OTH AF: 0.0858

Alfa AF: 0.0832 Hom.: 109

Bravo AF: 0.110

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	0.28
Dann	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs243757; hg19: chr6-54385981;