rs7541884

Variant names:

• chr1-188422098-A-C
• rs7541884

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 0.887 in 152,256 control chromosomes in the GnomAD database, including 60,087 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 0.89 (60087 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.771
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.901 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: 0.887 AC: 134997 AN: 152138 Hom.: 60047 Cov.: 33

Gnomad AFR AF: 0.864

Gnomad AMI AF: 0.959

Gnomad AMR AF: 0.889

Gnomad ASJ AF: 0.854

Gnomad EAS AF: 0.755

Gnomad SAS AF: 0.877

Gnomad FIN AF: 0.930

Gnomad MID AF: 0.861

Gnomad NFE AF: 0.907

Gnomad OTH AF: 0.875

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

GnomAD4 genome AF: 0.887 AC: 135094 AN: 152256 Hom.: 60087 Cov.: 33 AF XY: 0.887 AC XY: 66015 AN XY: 74432

African (AFR) AF: 0.864 AC: 35884 AN: 41542

American (AMR) AF: 0.890 AC: 13606 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.854 AC: 2966 AN: 3472

East Asian (EAS) AF: 0.754 AC: 3903 AN: 5176

South Asian (SAS) AF: 0.877 AC: 4230 AN: 4824

European-Finnish (FIN) AF: 0.930 AC: 9856 AN: 10596

Middle Eastern (MID) AF: 0.861 AC: 253 AN: 294

European-Non Finnish (NFE) AF: 0.907 AC: 61671 AN: 68030

Other (OTH) AF: 0.875 AC: 1850 AN: 2114

Alfa AF: 0.900 Hom.: 76981

Bravo AF: 0.885

Asia WGS AF: 0.836 AC: 2907 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.22
DANN	Benign	0.42
PhyloP100		-0.77

Splicing

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

Other links and lift over

dbSNP: rs7541884; hg19: chr1-188391229;