rs661827

Positions:

• chr13-68850619-C-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 0.224 in 151,956 control chromosomes in the GnomAD database, including 4,168 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 0.22 (4168 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.676

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.267 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: 0.224 AC: 33958 AN: 151838 Hom.: 4161 Cov.: 32

Gnomad AFR AF: 0.187

Gnomad AMI AF: 0.161

Gnomad AMR AF: 0.199

Gnomad ASJ AF: 0.314

Gnomad EAS AF: 0.00251

Gnomad SAS AF: 0.103

Gnomad FIN AF: 0.238

Gnomad MID AF: 0.250

Gnomad NFE AF: 0.270

Gnomad OTH AF: 0.246

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

GnomAD4 genome AF: 0.224 AC: 34002 AN: 151956 Hom.: 4168 Cov.: 32 AF XY: 0.219 AC XY: 16235 AN XY: 74252

Gnomad4 AFR AF: 0.187

Gnomad4 AMR AF: 0.199

Gnomad4 ASJ AF: 0.314

Gnomad4 EAS AF: 0.00251

Gnomad4 SAS AF: 0.104

Gnomad4 FIN AF: 0.238

Gnomad4 NFE AF: 0.270

Gnomad4 OTH AF: 0.243

Alfa AF: 0.261 Hom.: 10054

Bravo AF: 0.221

Asia WGS AF: 0.0670 AC: 235 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.16
DANN	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs661827; hg19: chr13-69424751;