20-50446576-G-A

Variant names:

• chr20-50446576-G-A
• rs11696955

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.0916 in 152,200 control chromosomes in the GnomAD database, including 968 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 0.092 (968 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.130
• Publications: 6 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.191 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0913 AC: 13890 AN: 152082 Hom.: 961 Cov.: 33

Gnomad AFR AF: 0.195

Gnomad AMI AF: 0.0274

Gnomad AMR AF: 0.0644

Gnomad ASJ AF: 0.0988

Gnomad EAS AF: 0.0824

Gnomad SAS AF: 0.0236

Gnomad FIN AF: 0.0199

Gnomad MID AF: 0.0665

Gnomad NFE AF: 0.0515

Gnomad OTH AF: 0.0965

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

GnomAD4 genome AF: 0.0916 AC: 13939 AN: 152200 Hom.: 968 Cov.: 33 AF XY: 0.0869 AC XY: 6464 AN XY: 74414

African (AFR) AF: 0.195 AC: 8093 AN: 41496

American (AMR) AF: 0.0643 AC: 983 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.0988 AC: 343 AN: 3470

East Asian (EAS) AF: 0.0826 AC: 427 AN: 5170

South Asian (SAS) AF: 0.0243 AC: 117 AN: 4822

European-Finnish (FIN) AF: 0.0199 AC: 211 AN: 10610

Middle Eastern (MID) AF: 0.0646 AC: 19 AN: 294

European-Non Finnish (NFE) AF: 0.0515 AC: 3503 AN: 68020

Other (OTH) AF: 0.103 AC: 218 AN: 2116

Alfa AF: 0.0685 Hom.: 1127

Bravo AF: 0.100

Asia WGS AF: 0.0890 AC: 310 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.3
DANN	Benign	0.76
PhyloP100		-0.13

Splicing

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

Other links and lift over

dbSNP: rs11696955; hg19: chr20-49063113;