7-45128344-G-C

Variant names:

• chr7-45128344-G-C
• rs2119050

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 0.466 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.466 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

Gnomad4 AFR AF: 0.568

Gnomad4 AMR AF: 0.448

Gnomad4 ASJ AF: 0.492

Gnomad4 EAS AF: 0.328

Gnomad4 SAS AF: 0.537

Gnomad4 FIN AF: 0.368

Gnomad4 NFE AF: 0.431

Gnomad4 OTH AF: 0.431

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 v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2119050; hg19: chr7-45167943;