rs964216

Variant names:

• chr20-16645437-C-T
• rs964216

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 0.213 in 152,130 control chromosomes in the GnomAD database, including 4,921 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 0.21 (4921 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.53
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.419 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: 0.213 AC: 32305 AN: 152012 Hom.: 4910 Cov.: 33

Gnomad AFR AF: 0.425

Gnomad AMI AF: 0.152

Gnomad AMR AF: 0.194

Gnomad ASJ AF: 0.102

Gnomad EAS AF: 0.239

Gnomad SAS AF: 0.247

Gnomad FIN AF: 0.127

Gnomad MID AF: 0.0955

Gnomad NFE AF: 0.104

Gnomad OTH AF: 0.185

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

GnomAD4 genome AF: 0.213 AC: 32355 AN: 152130 Hom.: 4921 Cov.: 33 AF XY: 0.213 AC XY: 15833 AN XY: 74378

African (AFR) AF: 0.424 AC: 17602 AN: 41476

American (AMR) AF: 0.194 AC: 2966 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.102 AC: 355 AN: 3468

East Asian (EAS) AF: 0.239 AC: 1236 AN: 5174

South Asian (SAS) AF: 0.246 AC: 1186 AN: 4820

European-Finnish (FIN) AF: 0.127 AC: 1341 AN: 10588

Middle Eastern (MID) AF: 0.0890 AC: 26 AN: 292

European-Non Finnish (NFE) AF: 0.104 AC: 7105 AN: 68004

Other (OTH) AF: 0.189 AC: 400 AN: 2112

Alfa AF: 0.135 Hom.: 2841

Bravo AF: 0.227

Asia WGS AF: 0.275 AC: 953 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.41
DANN	Benign	0.33
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs964216; hg19: chr20-16626082;