rs7779057

Variant names:

• chr7-106954440-C-T
• rs7779057

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 0.244 in 151,884 control chromosomes in the GnomAD database, including 5,073 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 0.24 (5073 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.404

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 = 0.363 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: 0.244 AC: 37015 AN: 151766 Hom.: 5043 Cov.: 31

Gnomad AFR AF: 0.367

Gnomad AMI AF: 0.288

Gnomad AMR AF: 0.195

Gnomad ASJ AF: 0.165

Gnomad EAS AF: 0.0642

Gnomad SAS AF: 0.133

Gnomad FIN AF: 0.221

Gnomad MID AF: 0.177

Gnomad NFE AF: 0.210

Gnomad OTH AF: 0.210

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

GnomAD4 genome AF: 0.244 AC: 37102 AN: 151884 Hom.: 5073 Cov.: 31 AF XY: 0.241 AC XY: 17855 AN XY: 74230

Gnomad4 AFR AF: 0.368

Gnomad4 AMR AF: 0.195

Gnomad4 ASJ AF: 0.165

Gnomad4 EAS AF: 0.0642

Gnomad4 SAS AF: 0.132

Gnomad4 FIN AF: 0.221

Gnomad4 NFE AF: 0.210

Gnomad4 OTH AF: 0.214

Alfa AF: 0.214 Hom.: 1727

Bravo AF: 0.248

Asia WGS AF: 0.139 AC: 481 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	1.2
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: rs7779057; hg19: chr7-106594885;