rs1406966

Variant names:

• chr20-40157403-G-A
• rs1406966

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 0.163 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.162 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

Gnomad4 AFR AF: 0.191

Gnomad4 AMR AF: 0.0981

Gnomad4 ASJ AF: 0.149

Gnomad4 EAS AF: 0.118

Gnomad4 SAS AF: 0.143

Gnomad4 FIN AF: 0.202

Gnomad4 NFE AF: 0.161

Gnomad4 OTH AF: 0.158

Alfa AF: 0.153 Hom.: 574

Bravo AF: 0.156

Asia WGS AF: 0.154 AC: 535 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1406966; hg19: chr20-38786044;