rs6711016

Positions:

• chr2-20923592-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 0.2 in 152,140 control chromosomes in the GnomAD database, including 3,972 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 0.20 (3972 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.64

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.532 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: 0.200 AC: 30463 AN: 152022 Hom.: 3975 Cov.: 33

Gnomad AFR AF: 0.0580

Gnomad AMI AF: 0.227

Gnomad AMR AF: 0.224

Gnomad ASJ AF: 0.163

Gnomad EAS AF: 0.550

Gnomad SAS AF: 0.368

Gnomad FIN AF: 0.276

Gnomad MID AF: 0.313

Gnomad NFE AF: 0.232

Gnomad OTH AF: 0.217

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

GnomAD4 genome AF: 0.200 AC: 30453 AN: 152140 Hom.: 3972 Cov.: 33 AF XY: 0.206 AC XY: 15324 AN XY: 74372

Gnomad4 AFR AF: 0.0578

Gnomad4 AMR AF: 0.224

Gnomad4 ASJ AF: 0.163

Gnomad4 EAS AF: 0.549

Gnomad4 SAS AF: 0.366

Gnomad4 FIN AF: 0.276

Gnomad4 NFE AF: 0.232

Gnomad4 OTH AF: 0.224

Alfa AF: 0.231 Hom.: 4711

Bravo AF: 0.189

Asia WGS AF: 0.445 AC: 1543 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	13
DANN	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6711016; hg19: chr2-21123352;