rs259822

Variant names:

• chr2-179910977-A-G
• rs259822
• ENST00000807586.1:n.241-6376A>G

Your query was ambiguous. Multiple possible variants found:

• chr2-179910977-A-G
• chr2-179910977-A-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000807586.1(ENSG00000304992):​n.241-6376A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.43 in 152,068 control chromosomes in the GnomAD database, including 15,756 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 0.43 (15756 hom., cov: 33)
• Consequence: ENSG00000304992 ENST00000807586.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0160
• Publications: 1 publications found

Genes affected

ENSG00000304992 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.654 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000807586.1. You can select a different transcript below to see updated ACMG assignments.

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
	ENSG00000304992	ENST00000807586.1		n.241-6376A>G		intron	N/A
	ENSG00000304992	ENST00000807587.1		n.172-6376A>G		intron	N/A
	ENSG00000304992	ENST00000807588.1		n.94-393A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.430 AC: 65334 AN: 151950 Hom.: 15722 Cov.: 33

Gnomad AFR AF: 0.661

Gnomad AMI AF: 0.310

Gnomad AMR AF: 0.424

Gnomad ASJ AF: 0.305

Gnomad EAS AF: 0.158

Gnomad SAS AF: 0.277

Gnomad FIN AF: 0.400

Gnomad MID AF: 0.268

Gnomad NFE AF: 0.337

Gnomad OTH AF: 0.390

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

GnomAD4 genome AF: 0.430 AC: 65415 AN: 152068 Hom.: 15756 Cov.: 33 AF XY: 0.429 AC XY: 31865 AN XY: 74318

African (AFR) AF: 0.661 AC: 27405 AN: 41468

American (AMR) AF: 0.425 AC: 6489 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.305 AC: 1058 AN: 3472

East Asian (EAS) AF: 0.158 AC: 815 AN: 5164

South Asian (SAS) AF: 0.276 AC: 1332 AN: 4820

European-Finnish (FIN) AF: 0.400 AC: 4227 AN: 10564

Middle Eastern (MID) AF: 0.260 AC: 76 AN: 292

European-Non Finnish (NFE) AF: 0.337 AC: 22913 AN: 67984

Other (OTH) AF: 0.387 AC: 818 AN: 2114

Alfa AF: 0.359 Hom.: 37674

Bravo AF: 0.445

Asia WGS AF: 0.259 AC: 902 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	4.7
DANN	Benign	0.72
PhyloP100		0.016

Splicing

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

Other links and lift over

dbSNP: rs259822; hg19: chr2-180775704;