rs204247

Positions:

• chr6-13722291-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 0.584 in 152,064 control chromosomes in the GnomAD database, including 26,119 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 0.58 (26119 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.19

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.657 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: 0.584 AC: 88720 AN: 151946 Hom.: 26071 Cov.: 33

Gnomad AFR AF: 0.663

Gnomad AMI AF: 0.482

Gnomad AMR AF: 0.571

Gnomad ASJ AF: 0.583

Gnomad EAS AF: 0.410

Gnomad SAS AF: 0.555

Gnomad FIN AF: 0.558

Gnomad MID AF: 0.557

Gnomad NFE AF: 0.560

Gnomad OTH AF: 0.564

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

GnomAD4 genome AF: 0.584 AC: 88829 AN: 152064 Hom.: 26119 Cov.: 33 AF XY: 0.582 AC XY: 43271 AN XY: 74310

Gnomad4 AFR AF: 0.663

Gnomad4 AMR AF: 0.571

Gnomad4 ASJ AF: 0.583

Gnomad4 EAS AF: 0.411

Gnomad4 SAS AF: 0.557

Gnomad4 FIN AF: 0.558

Gnomad4 NFE AF: 0.560

Gnomad4 OTH AF: 0.563

Alfa AF: 0.573 Hom.: 15392

Bravo AF: 0.588

Asia WGS AF: 0.525 AC: 1829 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.0080
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: rs204247; hg19: chr6-13722523;