rs300780

Variant names:

• chr2-110819-C-T
• rs300780

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 0.443 in 151,990 control chromosomes in the GnomAD database, including 14,984 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 0.44 (14984 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0760
• Publications: 13 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.539 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.443 AC: 67247 AN: 151870 Hom.: 14984 Cov.: 33

Gnomad AFR AF: 0.438

Gnomad AMI AF: 0.403

Gnomad AMR AF: 0.423

Gnomad ASJ AF: 0.461

Gnomad EAS AF: 0.556

Gnomad SAS AF: 0.332

Gnomad FIN AF: 0.535

Gnomad MID AF: 0.453

Gnomad NFE AF: 0.435

Gnomad OTH AF: 0.442

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

GnomAD4 genome AF: 0.443 AC: 67271 AN: 151990 Hom.: 14984 Cov.: 33 AF XY: 0.444 AC XY: 33019 AN XY: 74312

African (AFR) AF: 0.438 AC: 18147 AN: 41462

American (AMR) AF: 0.422 AC: 6450 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.461 AC: 1598 AN: 3468

East Asian (EAS) AF: 0.556 AC: 2879 AN: 5178

South Asian (SAS) AF: 0.331 AC: 1594 AN: 4822

European-Finnish (FIN) AF: 0.535 AC: 5634 AN: 10538

Middle Eastern (MID) AF: 0.446 AC: 131 AN: 294

European-Non Finnish (NFE) AF: 0.435 AC: 29547 AN: 67936

Other (OTH) AF: 0.438 AC: 924 AN: 2112

Alfa AF: 0.432 Hom.: 14122

Bravo AF: 0.436

Asia WGS AF: 0.412 AC: 1423 AN: 3456

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.98
DANN	Benign	0.65
PhyloP100		0.076

Splicing

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

Other links and lift over

dbSNP: rs300780; hg19: chr2-110819;