rs7541193

Variant names:

• chr1-153699771-G-T
• rs7541193

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 0.609 in 151,824 control chromosomes in the GnomAD database, including 28,982 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 0.61 (28982 hom., cov: 30)
• Consequence: GEMIN2P1 intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.869
• Publications: 9 publications found

Genes affected

GEMIN2P1 (HGNC:49561): (gem nuclear organelle associated protein 2 pseudogene 1)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.729 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: 0.608 AC: 92272 AN: 151704 Hom.: 28930 Cov.: 30

Gnomad AFR AF: 0.736

Gnomad AMI AF: 0.366

Gnomad AMR AF: 0.688

Gnomad ASJ AF: 0.443

Gnomad EAS AF: 0.736

Gnomad SAS AF: 0.620

Gnomad FIN AF: 0.478

Gnomad MID AF: 0.585

Gnomad NFE AF: 0.535

Gnomad OTH AF: 0.592

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

GnomAD4 genome AF: 0.609 AC: 92388 AN: 151824 Hom.: 28982 Cov.: 30 AF XY: 0.609 AC XY: 45187 AN XY: 74184

African (AFR) AF: 0.736 AC: 30468 AN: 41394

American (AMR) AF: 0.689 AC: 10501 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.443 AC: 1536 AN: 3470

East Asian (EAS) AF: 0.737 AC: 3807 AN: 5166

South Asian (SAS) AF: 0.620 AC: 2987 AN: 4814

European-Finnish (FIN) AF: 0.478 AC: 5022 AN: 10500

Middle Eastern (MID) AF: 0.599 AC: 176 AN: 294

European-Non Finnish (NFE) AF: 0.535 AC: 36319 AN: 67934

Other (OTH) AF: 0.590 AC: 1240 AN: 2100

Alfa AF: 0.562 Hom.: 18874

Bravo AF: 0.630

Asia WGS AF: 0.656 AC: 2283 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.30
DANN	Benign	0.30
PhyloP100		-0.87

Splicing

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

Other links and lift over

dbSNP: rs7541193; hg19: chr1-153672247;