rs7543680

Variant names:

• chr1-22404776-G-A
• rs7543680

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 18 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.405 AC: 16777 AN: 41466

American (AMR) AF: 0.177 AC: 2703 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.218 AC: 755 AN: 3470

East Asian (EAS) AF: 0.252 AC: 1303 AN: 5166

South Asian (SAS) AF: 0.274 AC: 1323 AN: 4824

European-Finnish (FIN) AF: 0.168 AC: 1777 AN: 10588

Middle Eastern (MID) AF: 0.272 AC: 80 AN: 294

European-Non Finnish (NFE) AF: 0.216 AC: 14682 AN: 68002

Other (OTH) AF: 0.246 AC: 519 AN: 2106

Alfa AF: 0.231 Hom.: 18520

Bravo AF: 0.270

Asia WGS AF: 0.253 AC: 883 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.20
DANN	Benign	0.62
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs7543680; hg19: chr1-22731269;