7-45925396-G-T

Variant names:

• chr7-45925396-G-T
• rs903889

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 0.788 in 152,148 control chromosomes in the GnomAD database, including 47,979 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 0.79 (47979 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.923

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 = 0.891 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: 0.788 AC: 119815 AN: 152030 Hom.: 47942 Cov.: 32

Gnomad AFR AF: 0.899

Gnomad AMI AF: 0.839

Gnomad AMR AF: 0.620

Gnomad ASJ AF: 0.867

Gnomad EAS AF: 0.786

Gnomad SAS AF: 0.777

Gnomad FIN AF: 0.636

Gnomad MID AF: 0.861

Gnomad NFE AF: 0.778

Gnomad OTH AF: 0.795

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

GnomAD4 genome AF: 0.788 AC: 119902 AN: 152148 Hom.: 47979 Cov.: 32 AF XY: 0.779 AC XY: 57895 AN XY: 74352

Gnomad4 AFR AF: 0.899

Gnomad4 AMR AF: 0.619

Gnomad4 ASJ AF: 0.867

Gnomad4 EAS AF: 0.786

Gnomad4 SAS AF: 0.777

Gnomad4 FIN AF: 0.636

Gnomad4 NFE AF: 0.778

Gnomad4 OTH AF: 0.798

Alfa AF: 0.769 Hom.: 9517

Bravo AF: 0.790

Asia WGS AF: 0.764 AC: 2656 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	0.19
DANN	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs903889; hg19: chr7-45964995;