rs1406966

Variant names:

• chr20-40157403-G-A
• rs1406966

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 0.163 in 152,072 control chromosomes in the GnomAD database, including 2,112 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 0.16 (2112 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.75
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.188 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.162 AC: 24688 AN: 151954 Hom.: 2099 Cov.: 32

Gnomad AFR AF: 0.191

Gnomad AMI AF: 0.0921

Gnomad AMR AF: 0.0983

Gnomad ASJ AF: 0.149

Gnomad EAS AF: 0.118

Gnomad SAS AF: 0.143

Gnomad FIN AF: 0.202

Gnomad MID AF: 0.0633

Gnomad NFE AF: 0.161

Gnomad OTH AF: 0.157

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

GnomAD4 genome AF: 0.163 AC: 24740 AN: 152072 Hom.: 2112 Cov.: 32 AF XY: 0.161 AC XY: 11931 AN XY: 74300

African (AFR) AF: 0.191 AC: 7926 AN: 41450

American (AMR) AF: 0.0981 AC: 1500 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.149 AC: 517 AN: 3468

East Asian (EAS) AF: 0.118 AC: 611 AN: 5170

South Asian (SAS) AF: 0.143 AC: 689 AN: 4816

European-Finnish (FIN) AF: 0.202 AC: 2136 AN: 10580

Middle Eastern (MID) AF: 0.0612 AC: 18 AN: 294

European-Non Finnish (NFE) AF: 0.161 AC: 10925 AN: 67988

Other (OTH) AF: 0.158 AC: 334 AN: 2108

Alfa AF: 0.154 Hom.: 714

Bravo AF: 0.156

Asia WGS AF: 0.154 AC: 535 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.12
DANN	Benign	0.58
PhyloP100		-1.8

Splicing

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

Other links and lift over

dbSNP: rs1406966; hg19: chr20-38786044;