rs1402045

chr4-12646781-G-Achr4-12646781-G-T

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 0.203 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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

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

Gnomad4 AFR AF: 0.0536

Gnomad4 AMR AF: 0.160

Gnomad4 ASJ AF: 0.398

Gnomad4 EAS AF: 0.00194

Gnomad4 SAS AF: 0.0998

Gnomad4 FIN AF: 0.312

Gnomad4 NFE AF: 0.299

Gnomad4 OTH AF: 0.202

Alfa AF: 0.267 Hom.: 1206

Bravo AF: 0.185

Asia WGS AF: 0.0480 AC: 170 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	2.6
Dann	Benign	0.18

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1402045; hg19: chr4-12648405;