7-45921946-T-C

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 0.789 in 163,106 control chromosomes in the GnomAD database, including 51,610 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 (48487 hom., cov: 34)
  • Exomes 𝑓: 0.75 (3123 hom.)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.257

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.9 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: 0.792 AC: 120441 AN: 152162 Hom.: 48439 Cov.: 34

Gnomad AFR AF: 0.908

Gnomad AMI AF: 0.839

Gnomad AMR AF: 0.627

Gnomad ASJ AF: 0.866

Gnomad EAS AF: 0.786

Gnomad SAS AF: 0.778

Gnomad FIN AF: 0.636

Gnomad MID AF: 0.870

Gnomad NFE AF: 0.778

Gnomad OTH AF: 0.797

GnomAD4 exome AF: 0.751 AC: 8130 AN: 10826 Hom.: 3123 AF XY: 0.762 AC XY: 4655 AN XY: 6110

Gnomad4 AFR exome AF: 0.948

Gnomad4 AMR exome AF: 0.455

Gnomad4 ASJ exome AF: 0.908

Gnomad4 EAS exome AF: 0.883

Gnomad4 SAS exome AF: 0.779

Gnomad4 FIN exome AF: 0.609

Gnomad4 NFE exome AF: 0.755

Gnomad4 OTH exome AF: 0.773

GnomAD4 genome AF: 0.792 AC: 120540 AN: 152280 Hom.: 48487 Cov.: 34 AF XY: 0.782 AC XY: 58224 AN XY: 74438

Gnomad4 AFR AF: 0.908

Gnomad4 AMR AF: 0.627

Gnomad4 ASJ AF: 0.866

Gnomad4 EAS AF: 0.787

Gnomad4 SAS AF: 0.778

Gnomad4 FIN AF: 0.636

Gnomad4 NFE AF: 0.778

Gnomad4 OTH AF: 0.799

Alfa AF: 0.804 Hom.: 7627

Bravo AF: 0.793

Asia WGS AF: 0.771 AC: 2682 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
Cadd	Benign	6.2
Dann	Benign	0.29

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2132572; hg19: chr7-45961545;