rs7457114

Positions:

• chr7-12261960-A-G

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 0.812 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.812 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

Gnomad4 AFR AF: 0.941

Gnomad4 AMR AF: 0.791

Gnomad4 ASJ AF: 0.770

Gnomad4 EAS AF: 0.692

Gnomad4 SAS AF: 0.728

Gnomad4 FIN AF: 0.728

Gnomad4 NFE AF: 0.769

Gnomad4 OTH AF: 0.787

Alfa AF: 0.785 Hom.: 18592

Bravo AF: 0.825

Asia WGS AF: 0.730 AC: 2540 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7457114; hg19: chr7-12301586;