rs1861125

chr4-18293207-C-Gchr4-18293207-C-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 0.441 in 151,678 control chromosomes in the GnomAD database, including 15,359 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 0.44 (15359 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.38

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.559 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: 0.441 AC: 66768 AN: 151560 Hom.: 15326 Cov.: 29

Gnomad AFR AF: 0.565

Gnomad AMI AF: 0.435

Gnomad AMR AF: 0.467

Gnomad ASJ AF: 0.348

Gnomad EAS AF: 0.530

Gnomad SAS AF: 0.436

Gnomad FIN AF: 0.315

Gnomad MID AF: 0.453

Gnomad NFE AF: 0.377

Gnomad OTH AF: 0.441

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

GnomAD4 genome AF: 0.441 AC: 66861 AN: 151678 Hom.: 15359 Cov.: 29 AF XY: 0.438 AC XY: 32470 AN XY: 74100

Gnomad4 AFR AF: 0.565

Gnomad4 AMR AF: 0.467

Gnomad4 ASJ AF: 0.348

Gnomad4 EAS AF: 0.529

Gnomad4 SAS AF: 0.436

Gnomad4 FIN AF: 0.315

Gnomad4 NFE AF: 0.377

Gnomad4 OTH AF: 0.444

Alfa AF: 0.216 Hom.: 394

Bravo AF: 0.460

Asia WGS AF: 0.521 AC: 1813 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
Cadd	Benign	0.093
Dann	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1861125; hg19: chr4-18294830;