rs1861125

Variant names:

• chr4-18293207-C-G
• rs1861125

Your query was ambiguous. Multiple possible variants found:

• chr4-18293207-C-G
• chr4-18293207-C-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 0.441 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
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• 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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.565 AC: 23359 AN: 41326

American (AMR) AF: 0.467 AC: 7122 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.348 AC: 1208 AN: 3468

East Asian (EAS) AF: 0.529 AC: 2711 AN: 5124

South Asian (SAS) AF: 0.436 AC: 2075 AN: 4760

European-Finnish (FIN) AF: 0.315 AC: 3320 AN: 10532

Middle Eastern (MID) AF: 0.463 AC: 136 AN: 294

European-Non Finnish (NFE) AF: 0.377 AC: 25598 AN: 67910

Other (OTH) AF: 0.444 AC: 937 AN: 2112

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
PhyloP100		-2.4

Splicing

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

Other links and lift over

dbSNP: rs1861125; hg19: chr4-18294830;