rs7525357

chr1-6240444-G-Cchr1-6240444-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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;