rs1402045

Variant names:

• chr4-12646781-G-A
• rs1402045

Your query was ambiguous. Multiple possible variants found:

• chr4-12646781-G-A
• chr4-12646781-G-T

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 0.203 in 151,868 control chromosomes in the GnomAD database, including 4,138 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 0.20 (4138 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.277
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.295 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: 0.203 AC: 30807 AN: 151750 Hom.: 4138 Cov.: 32

Gnomad AFR AF: 0.0538

Gnomad AMI AF: 0.248

Gnomad AMR AF: 0.160

Gnomad ASJ AF: 0.398

Gnomad EAS AF: 0.00193

Gnomad SAS AF: 0.0999

Gnomad FIN AF: 0.312

Gnomad MID AF: 0.162

Gnomad NFE AF: 0.299

Gnomad OTH AF: 0.205

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

GnomAD4 genome AF: 0.203 AC: 30806 AN: 151868 Hom.: 4138 Cov.: 32 AF XY: 0.199 AC XY: 14768 AN XY: 74196

African (AFR) AF: 0.0536 AC: 2224 AN: 41468

American (AMR) AF: 0.160 AC: 2430 AN: 15188

Ashkenazi Jewish (ASJ) AF: 0.398 AC: 1379 AN: 3466

East Asian (EAS) AF: 0.00194 AC: 10 AN: 5158

South Asian (SAS) AF: 0.0998 AC: 480 AN: 4812

European-Finnish (FIN) AF: 0.312 AC: 3287 AN: 10540

Middle Eastern (MID) AF: 0.185 AC: 54 AN: 292

European-Non Finnish (NFE) AF: 0.299 AC: 20291 AN: 67928

Other (OTH) AF: 0.202 AC: 425 AN: 2104

Alfa AF: 0.261 Hom.: 1209

Bravo AF: 0.185

Asia WGS AF: 0.0480 AC: 170 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.6
DANN	Benign	0.18
PhyloP100		0.28

Splicing

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

Other links and lift over

dbSNP: rs1402045; hg19: chr4-12648405;