rs7543680

chr1-22404776-G-A

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 0.264 in 152,108 control chromosomes in the GnomAD database, including 5,997 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 0.26 (5997 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.23

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.399 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: 0.264 AC: 40057 AN: 151990 Hom.: 5990 Cov.: 32

Gnomad AFR AF: 0.405

Gnomad AMI AF: 0.191

Gnomad AMR AF: 0.177

Gnomad ASJ AF: 0.218

Gnomad EAS AF: 0.252

Gnomad SAS AF: 0.275

Gnomad FIN AF: 0.168

Gnomad MID AF: 0.272

Gnomad NFE AF: 0.216

Gnomad OTH AF: 0.246

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

GnomAD4 genome AF: 0.264 AC: 40092 AN: 152108 Hom.: 5997 Cov.: 32 AF XY: 0.258 AC XY: 19210 AN XY: 74358

Gnomad4 AFR AF: 0.405

Gnomad4 AMR AF: 0.177

Gnomad4 ASJ AF: 0.218

Gnomad4 EAS AF: 0.252

Gnomad4 SAS AF: 0.274

Gnomad4 FIN AF: 0.168

Gnomad4 NFE AF: 0.216

Gnomad4 OTH AF: 0.246

Alfa AF: 0.223 Hom.: 8129

Bravo AF: 0.270

Asia WGS AF: 0.253 AC: 883 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	0.20
Dann	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7543680; hg19: chr1-22731269;