7-45128344-G-C

Variant names:

• chr7-45128344-G-C
• rs2119050

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 0.466 in 151,780 control chromosomes in the GnomAD database, including 16,954 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 0.47 (16954 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0180
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.562 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: 0.466 AC: 70726 AN: 151662 Hom.: 16930 Cov.: 31

Gnomad AFR AF: 0.567

Gnomad AMI AF: 0.407

Gnomad AMR AF: 0.448

Gnomad ASJ AF: 0.492

Gnomad EAS AF: 0.329

Gnomad SAS AF: 0.537

Gnomad FIN AF: 0.368

Gnomad MID AF: 0.408

Gnomad NFE AF: 0.431

Gnomad OTH AF: 0.432

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

GnomAD4 genome AF: 0.466 AC: 70797 AN: 151780 Hom.: 16954 Cov.: 31 AF XY: 0.462 AC XY: 34278 AN XY: 74160

African (AFR) AF: 0.568 AC: 23482 AN: 41356

American (AMR) AF: 0.448 AC: 6835 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.492 AC: 1707 AN: 3472

East Asian (EAS) AF: 0.328 AC: 1692 AN: 5158

South Asian (SAS) AF: 0.537 AC: 2589 AN: 4822

European-Finnish (FIN) AF: 0.368 AC: 3855 AN: 10486

Middle Eastern (MID) AF: 0.398 AC: 117 AN: 294

European-Non Finnish (NFE) AF: 0.431 AC: 29245 AN: 67922

Other (OTH) AF: 0.431 AC: 906 AN: 2104

Alfa AF: 0.454 Hom.: 1902

Bravo AF: 0.473

Asia WGS AF: 0.468 AC: 1630 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	6.4
DANN	Benign	0.54
PhyloP100		-0.018

Splicing

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

Other links and lift over

dbSNP: rs2119050; hg19: chr7-45167943;