rs1122780

Variant names:

• chr7-45388930-A-G
• rs1122780

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 0.278 in 152,150 control chromosomes in the GnomAD database, including 6,172 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 0.28 (6172 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.429

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.372 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: 0.278 AC: 42298 AN: 152032 Hom.: 6164 Cov.: 32

Gnomad AFR AF: 0.377

Gnomad AMI AF: 0.232

Gnomad AMR AF: 0.240

Gnomad ASJ AF: 0.243

Gnomad EAS AF: 0.111

Gnomad SAS AF: 0.189

Gnomad FIN AF: 0.268

Gnomad MID AF: 0.301

Gnomad NFE AF: 0.250

Gnomad OTH AF: 0.273

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

GnomAD4 genome AF: 0.278 AC: 42348 AN: 152150 Hom.: 6172 Cov.: 32 AF XY: 0.276 AC XY: 20532 AN XY: 74370

Gnomad4 AFR AF: 0.377

Gnomad4 AMR AF: 0.240

Gnomad4 ASJ AF: 0.243

Gnomad4 EAS AF: 0.111

Gnomad4 SAS AF: 0.188

Gnomad4 FIN AF: 0.268

Gnomad4 NFE AF: 0.250

Gnomad4 OTH AF: 0.275

Alfa AF: 0.276 Hom.: 1318

Bravo AF: 0.283

Asia WGS AF: 0.193 AC: 668 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	7.1
DANN	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1122780; hg19: chr7-45428529;