rs2783711

Positions:

• chr1-26102373-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 0.231 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.231 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

Gnomad4 AFR AF: 0.421

Gnomad4 AMR AF: 0.161

Gnomad4 ASJ AF: 0.203

Gnomad4 EAS AF: 0.0168

Gnomad4 SAS AF: 0.0804

Gnomad4 FIN AF: 0.147

Gnomad4 NFE AF: 0.173

Gnomad4 OTH AF: 0.233

Alfa AF: 0.183 Hom.: 1632

Bravo AF: 0.242

Asia WGS AF: 0.0890 AC: 311 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2783711; hg19: chr1-26428864;