rs1525287

Positions:

• chr7-70981283-A-G
• chr7-70981283-A-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 0.858 in 152,150 control chromosomes in the GnomAD database, including 56,739 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 0.86 (56739 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.309

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.966 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.858 AC: 130505 AN: 152032 Hom.: 56719 Cov.: 32

Gnomad AFR AF: 0.706

Gnomad AMI AF: 0.953

Gnomad AMR AF: 0.911

Gnomad ASJ AF: 0.901

Gnomad EAS AF: 0.988

Gnomad SAS AF: 0.912

Gnomad FIN AF: 0.912

Gnomad MID AF: 0.911

Gnomad NFE AF: 0.912

Gnomad OTH AF: 0.888

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

GnomAD4 genome AF: 0.858 AC: 130576 AN: 152150 Hom.: 56739 Cov.: 32 AF XY: 0.862 AC XY: 64112 AN XY: 74400

Gnomad4 AFR AF: 0.706

Gnomad4 AMR AF: 0.912

Gnomad4 ASJ AF: 0.901

Gnomad4 EAS AF: 0.988

Gnomad4 SAS AF: 0.912

Gnomad4 FIN AF: 0.912

Gnomad4 NFE AF: 0.912

Gnomad4 OTH AF: 0.885

Alfa AF: 0.893 Hom.: 21016

Bravo AF: 0.854

Asia WGS AF: 0.902 AC: 3138 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	12
DANN	Benign	0.81

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1525287; hg19: chr7-70446269;