7-48920029-T-C

Variant names:

• chr7-48920029-T-C
• rs6583479

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 0.779 in 151,238 control chromosomes in the GnomAD database, including 45,913 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 0.78 (45913 hom., cov: 31)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.54

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.05).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.817 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: 0.779 AC: 117709 AN: 151122 Hom.: 45862 Cov.: 31

Gnomad AFR AF: 0.824

Gnomad AMI AF: 0.813

Gnomad AMR AF: 0.721

Gnomad ASJ AF: 0.771

Gnomad EAS AF: 0.775

Gnomad SAS AF: 0.755

Gnomad FIN AF: 0.789

Gnomad MID AF: 0.828

Gnomad NFE AF: 0.765

Gnomad OTH AF: 0.764

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

GnomAD4 genome AF: 0.779 AC: 117817 AN: 151238 Hom.: 45913 Cov.: 31 AF XY: 0.780 AC XY: 57670 AN XY: 73896

Gnomad4 AFR AF: 0.825

Gnomad4 AMR AF: 0.721

Gnomad4 ASJ AF: 0.771

Gnomad4 EAS AF: 0.774

Gnomad4 SAS AF: 0.753

Gnomad4 FIN AF: 0.789

Gnomad4 NFE AF: 0.765

Gnomad4 OTH AF: 0.766

Alfa AF: 0.689 Hom.: 1386

Bravo AF: 0.776

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.47
DANN	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6583479; hg19: chr7-48959625;