rs4280044

Variant names:

• chr12-77199458-G-A
• rs4280044

Your query was ambiguous. Multiple possible variants found:

• chr12-77199458-G-A
• chr12-77199458-G-T

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 0.781 in 151,952 control chromosomes in the GnomAD database, including 46,828 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 0.78 (46828 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.116
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.888 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.781 AC: 118585 AN: 151834 Hom.: 46777 Cov.: 32

Gnomad AFR AF: 0.896

Gnomad AMI AF: 0.693

Gnomad AMR AF: 0.737

Gnomad ASJ AF: 0.812

Gnomad EAS AF: 0.744

Gnomad SAS AF: 0.613

Gnomad FIN AF: 0.766

Gnomad MID AF: 0.736

Gnomad NFE AF: 0.738

Gnomad OTH AF: 0.772

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

GnomAD4 genome AF: 0.781 AC: 118693 AN: 151952 Hom.: 46828 Cov.: 32 AF XY: 0.777 AC XY: 57713 AN XY: 74262

African (AFR) AF: 0.896 AC: 37178 AN: 41498

American (AMR) AF: 0.737 AC: 11238 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.812 AC: 2819 AN: 3470

East Asian (EAS) AF: 0.745 AC: 3811 AN: 5116

South Asian (SAS) AF: 0.612 AC: 2943 AN: 4806

European-Finnish (FIN) AF: 0.766 AC: 8103 AN: 10574

Middle Eastern (MID) AF: 0.736 AC: 215 AN: 292

European-Non Finnish (NFE) AF: 0.738 AC: 50118 AN: 67932

Other (OTH) AF: 0.777 AC: 1637 AN: 2108

Alfa AF: 0.766 Hom.: 5491

Bravo AF: 0.786

Asia WGS AF: 0.724 AC: 2521 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	2.5
DANN	Benign	0.67
PhyloP100		0.12

Splicing

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

Other links and lift over

dbSNP: rs4280044; hg19: chr12-77593238;