rs2783711

Variant names:

• chr1-26102373-G-A
• rs2783711

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 0.231 in 152,090 control chromosomes in the GnomAD database, including 5,294 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 0.23 (5294 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.213
• Publications: 7 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.416 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: 0.231 AC: 35098 AN: 151972 Hom.: 5283 Cov.: 32

Gnomad AFR AF: 0.421

Gnomad AMI AF: 0.177

Gnomad AMR AF: 0.161

Gnomad ASJ AF: 0.203

Gnomad EAS AF: 0.0172

Gnomad SAS AF: 0.0813

Gnomad FIN AF: 0.147

Gnomad MID AF: 0.280

Gnomad NFE AF: 0.173

Gnomad OTH AF: 0.233

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

GnomAD4 genome AF: 0.231 AC: 35142 AN: 152090 Hom.: 5294 Cov.: 32 AF XY: 0.223 AC XY: 16597 AN XY: 74366

African (AFR) AF: 0.421 AC: 17475 AN: 41460

American (AMR) AF: 0.161 AC: 2461 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.203 AC: 704 AN: 3470

East Asian (EAS) AF: 0.0168 AC: 87 AN: 5170

South Asian (SAS) AF: 0.0804 AC: 388 AN: 4828

European-Finnish (FIN) AF: 0.147 AC: 1553 AN: 10590

Middle Eastern (MID) AF: 0.267 AC: 78 AN: 292

European-Non Finnish (NFE) AF: 0.173 AC: 11743 AN: 67998

Other (OTH) AF: 0.233 AC: 492 AN: 2108

Alfa AF: 0.182 Hom.: 2612

Bravo AF: 0.242

Asia WGS AF: 0.0890 AC: 311 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.3
DANN	Benign	0.44
PhyloP100		0.21

Splicing

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

Other links and lift over

dbSNP: rs2783711; hg19: chr1-26428864;