7-12261960-A-G

Variant names:

• chr7-12261960-A-G
• rs7457114

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 0.812 in 151,698 control chromosomes in the GnomAD database, including 50,591 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 0.81 (50591 hom., cov: 28)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.297
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.933 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.812 AC: 123082 AN: 151580 Hom.: 50538 Cov.: 28

Gnomad AFR AF: 0.941

Gnomad AMI AF: 0.823

Gnomad AMR AF: 0.791

Gnomad ASJ AF: 0.770

Gnomad EAS AF: 0.691

Gnomad SAS AF: 0.728

Gnomad FIN AF: 0.728

Gnomad MID AF: 0.803

Gnomad NFE AF: 0.769

Gnomad OTH AF: 0.789

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

GnomAD4 genome AF: 0.812 AC: 123196 AN: 151698 Hom.: 50591 Cov.: 28 AF XY: 0.809 AC XY: 59957 AN XY: 74096

African (AFR) AF: 0.941 AC: 38942 AN: 41382

American (AMR) AF: 0.791 AC: 12057 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.770 AC: 2672 AN: 3468

East Asian (EAS) AF: 0.692 AC: 3568 AN: 5156

South Asian (SAS) AF: 0.728 AC: 3490 AN: 4792

European-Finnish (FIN) AF: 0.728 AC: 7611 AN: 10460

Middle Eastern (MID) AF: 0.798 AC: 233 AN: 292

European-Non Finnish (NFE) AF: 0.769 AC: 52212 AN: 67874

Other (OTH) AF: 0.787 AC: 1662 AN: 2112

Alfa AF: 0.786 Hom.: 22481

Bravo AF: 0.825

Asia WGS AF: 0.730 AC: 2540 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	2.2
DANN	Benign	0.61
PhyloP100		-0.30

Splicing

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

Other links and lift over

dbSNP: rs7457114; hg19: chr7-12301586;