rs11697325

chr20-46000706-G-Achr20-46000706-G-C

Variant summary

Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4 BA1

The variant allele was found at a frequency of 0.47 in 152,068 control chromosomes in the GnomAD database, including 18,705 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 0.47 (18705 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.92

ACMG classification

Verdict is Benign. Variant got -9 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.16).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.593 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: 0.470 AC: 71424 AN: 151948 Hom.: 18704 Cov.: 32

Gnomad AFR AF: 0.293

Gnomad AMI AF: 0.650

Gnomad AMR AF: 0.513

Gnomad ASJ AF: 0.563

Gnomad EAS AF: 0.0339

Gnomad SAS AF: 0.336

Gnomad FIN AF: 0.500

Gnomad MID AF: 0.586

Gnomad NFE AF: 0.597

Gnomad OTH AF: 0.511

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

GnomAD4 genome AF: 0.470 AC: 71434 AN: 152068 Hom.: 18705 Cov.: 32 AF XY: 0.461 AC XY: 34255 AN XY: 74312

Gnomad4 AFR AF: 0.292

Gnomad4 AMR AF: 0.513

Gnomad4 ASJ AF: 0.563

Gnomad4 EAS AF: 0.0336

Gnomad4 SAS AF: 0.338

Gnomad4 FIN AF: 0.500

Gnomad4 NFE AF: 0.597

Gnomad4 OTH AF: 0.505

Alfa AF: 0.368 Hom.: 1007

Bravo AF: 0.460

Asia WGS AF: 0.186 AC: 650 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.16
Cadd	Benign	21
Dann	Benign	0.85

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11697325; hg19: chr20-44629345;