rs1011725

Variant names:

• chr4-123470542-G-A
• rs1011725

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 0.165 in 152,120 control chromosomes in the GnomAD database, including 2,688 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 0.16 (2688 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0130
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.294 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.164 AC: 25002 AN: 152002 Hom.: 2680 Cov.: 33

Gnomad AFR AF: 0.298

Gnomad AMI AF: 0.0844

Gnomad AMR AF: 0.144

Gnomad ASJ AF: 0.0602

Gnomad EAS AF: 0.0959

Gnomad SAS AF: 0.152

Gnomad FIN AF: 0.161

Gnomad MID AF: 0.0696

Gnomad NFE AF: 0.103

Gnomad OTH AF: 0.120

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

GnomAD4 genome AF: 0.165 AC: 25030 AN: 152120 Hom.: 2688 Cov.: 33 AF XY: 0.166 AC XY: 12366 AN XY: 74382

African (AFR) AF: 0.298 AC: 12354 AN: 41466

American (AMR) AF: 0.144 AC: 2201 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.0602 AC: 209 AN: 3470

East Asian (EAS) AF: 0.0963 AC: 499 AN: 5182

South Asian (SAS) AF: 0.151 AC: 729 AN: 4816

European-Finnish (FIN) AF: 0.161 AC: 1707 AN: 10580

Middle Eastern (MID) AF: 0.0714 AC: 21 AN: 294

European-Non Finnish (NFE) AF: 0.103 AC: 6983 AN: 68008

Other (OTH) AF: 0.118 AC: 250 AN: 2112

Alfa AF: 0.126 Hom.: 558

Bravo AF: 0.167

Asia WGS AF: 0.127 AC: 439 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	3.3
DANN	Benign	0.54
PhyloP100		0.013

Splicing

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

Other links and lift over

dbSNP: rs1011725; hg19: chr4-124391697;