chr2-166616406-A-G

Variant names:

• chr2-166616406-A-G
• rs10183984

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 0.106 in 152,228 control chromosomes in the GnomAD database, including 1,045 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 0.11 (1045 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.806
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.171 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: 0.106 AC: 16175 AN: 152110 Hom.: 1044 Cov.: 32

Gnomad AFR AF: 0.141

Gnomad AMI AF: 0.206

Gnomad AMR AF: 0.0710

Gnomad ASJ AF: 0.132

Gnomad EAS AF: 0.00270

Gnomad SAS AF: 0.182

Gnomad FIN AF: 0.0413

Gnomad MID AF: 0.146

Gnomad NFE AF: 0.103

Gnomad OTH AF: 0.107

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

GnomAD4 genome AF: 0.106 AC: 16192 AN: 152228 Hom.: 1045 Cov.: 32 AF XY: 0.104 AC XY: 7762 AN XY: 74440

African (AFR) AF: 0.141 AC: 5845 AN: 41528

American (AMR) AF: 0.0707 AC: 1083 AN: 15308

Ashkenazi Jewish (ASJ) AF: 0.132 AC: 456 AN: 3466

East Asian (EAS) AF: 0.00289 AC: 15 AN: 5182

South Asian (SAS) AF: 0.181 AC: 876 AN: 4832

European-Finnish (FIN) AF: 0.0413 AC: 439 AN: 10622

Middle Eastern (MID) AF: 0.146 AC: 43 AN: 294

European-Non Finnish (NFE) AF: 0.103 AC: 7017 AN: 67976

Other (OTH) AF: 0.109 AC: 231 AN: 2114

Alfa AF: 0.104 Hom.: 1360

Bravo AF: 0.108

Asia WGS AF: 0.107 AC: 370 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	4.3
DANN	Benign	0.44
PhyloP100		0.81

Splicing

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

Other links and lift over

dbSNP: rs10183984; hg19: chr2-167472916;