chr7-70981283-A-G

Variant names:

• chr7-70981283-A-G
• rs1525287

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 0.858 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
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• 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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.706 AC: 29282 AN: 41460

American (AMR) AF: 0.912 AC: 13941 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.901 AC: 3127 AN: 3470

East Asian (EAS) AF: 0.988 AC: 5101 AN: 5162

South Asian (SAS) AF: 0.912 AC: 4398 AN: 4822

European-Finnish (FIN) AF: 0.912 AC: 9663 AN: 10594

Middle Eastern (MID) AF: 0.912 AC: 268 AN: 294

European-Non Finnish (NFE) AF: 0.912 AC: 62058 AN: 68032

Other (OTH) AF: 0.885 AC: 1869 AN: 2112

Alfa AF: 0.891 Hom.: 25558

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
PhyloP100		0.31

Splicing

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

Other links and lift over

dbSNP: rs1525287; hg19: chr7-70446269;