rs243802

chr6-54443919-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 0.102 in 152,120 control chromosomes in the GnomAD database, including 1,275 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 (1275 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.72

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.225 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: 0.102 AC: 15508 AN: 152002 Hom.: 1276 Cov.: 32

Gnomad AFR AF: 0.229

Gnomad AMI AF: 0.0307

Gnomad AMR AF: 0.0618

Gnomad ASJ AF: 0.0397

Gnomad EAS AF: 0.0149

Gnomad SAS AF: 0.0183

Gnomad FIN AF: 0.0305

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.0622

Gnomad OTH AF: 0.0875

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

GnomAD4 genome AF: 0.102 AC: 15520 AN: 152120 Hom.: 1275 Cov.: 32 AF XY: 0.0971 AC XY: 7222 AN XY: 74368

Gnomad4 AFR AF: 0.229

Gnomad4 AMR AF: 0.0617

Gnomad4 ASJ AF: 0.0397

Gnomad4 EAS AF: 0.0149

Gnomad4 SAS AF: 0.0181

Gnomad4 FIN AF: 0.0305

Gnomad4 NFE AF: 0.0622

Gnomad4 OTH AF: 0.0880

Alfa AF: 0.0860 Hom.: 108

Bravo AF: 0.111

Asia WGS AF: 0.0370 AC: 129 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	1.4
Dann	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs243802; hg19: chr6-54308717;