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. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.678 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

Gnomad4 AFR AF: 0.560

Gnomad4 AMR AF: 0.757

Gnomad4 ASJ AF: 0.747

Gnomad4 EAS AF: 0.572

Gnomad4 SAS AF: 0.673

Gnomad4 FIN AF: 0.755

Gnomad4 NFE AF: 0.725

Gnomad4 OTH AF: 0.696

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 v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7525357; hg19: chr1-6300504;