rs7525357

Variant names:

• chr1-6240444-G-C
• rs7525357

Your query was ambiguous. Multiple possible variants found:

• chr1-6240444-G-C
• chr1-6240444-G-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 0.678 in 152,002 control chromosomes in the GnomAD database, including 35,566 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 0.68 (35566 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0900
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.64).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.746 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: 0.678 AC: 103027 AN: 151884 Hom.: 35547 Cov.: 32

Gnomad AFR AF: 0.560

Gnomad AMI AF: 0.659

Gnomad AMR AF: 0.757

Gnomad ASJ AF: 0.747

Gnomad EAS AF: 0.571

Gnomad SAS AF: 0.673

Gnomad FIN AF: 0.755

Gnomad MID AF: 0.713

Gnomad NFE AF: 0.725

Gnomad OTH AF: 0.699

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

GnomAD4 genome AF: 0.678 AC: 103084 AN: 152002 Hom.: 35566 Cov.: 32 AF XY: 0.679 AC XY: 50466 AN XY: 74292

African (AFR) AF: 0.560 AC: 23197 AN: 41438

American (AMR) AF: 0.757 AC: 11563 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.747 AC: 2593 AN: 3470

East Asian (EAS) AF: 0.572 AC: 2954 AN: 5164

South Asian (SAS) AF: 0.673 AC: 3244 AN: 4818

European-Finnish (FIN) AF: 0.755 AC: 7972 AN: 10560

Middle Eastern (MID) AF: 0.726 AC: 212 AN: 292

European-Non Finnish (NFE) AF: 0.725 AC: 49281 AN: 67972

Other (OTH) AF: 0.696 AC: 1468 AN: 2110

Alfa AF: 0.707 Hom.: 4763

Bravo AF: 0.671

Asia WGS AF: 0.600 AC: 2082 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.64
CADD	Benign	4.5
DANN	Benign	0.54
PhyloP100		0.090

Splicing

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

Other links and lift over

dbSNP: rs7525357; hg19: chr1-6300504;