rs2685729

Variant names:

• chr2-81960228-T-C
• rs2685729
• ENST00000843045.1:n.303+26203A>G

Variant summary

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

The ENST00000843045.1(ENSG00000231781):​n.303+26203A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.675 in 151,460 control chromosomes in the GnomAD database, including 35,359 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 0.68 (35359 hom., cov: 29)
• Consequence: ENSG00000231781 ENST00000843045.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.209
• Publications: 1 publications found

Genes affected

ENSG00000231781 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.811 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
ENSG00000231781	ENST00000843045.1	n.303+26203A>G		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.675 AC: 102143 AN: 151344 Hom.: 35309 Cov.: 29

Gnomad AFR AF: 0.818

Gnomad AMI AF: 0.778

Gnomad AMR AF: 0.555

Gnomad ASJ AF: 0.652

Gnomad EAS AF: 0.413

Gnomad SAS AF: 0.554

Gnomad FIN AF: 0.678

Gnomad MID AF: 0.579

Gnomad NFE AF: 0.644

Gnomad OTH AF: 0.633

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

GnomAD4 genome AF: 0.675 AC: 102245 AN: 151460 Hom.: 35359 Cov.: 29 AF XY: 0.672 AC XY: 49655 AN XY: 73944

African (AFR) AF: 0.819 AC: 33841 AN: 41344

American (AMR) AF: 0.555 AC: 8444 AN: 15214

Ashkenazi Jewish (ASJ) AF: 0.652 AC: 2261 AN: 3466

East Asian (EAS) AF: 0.413 AC: 2107 AN: 5102

South Asian (SAS) AF: 0.554 AC: 2650 AN: 4784

European-Finnish (FIN) AF: 0.678 AC: 7056 AN: 10412

Middle Eastern (MID) AF: 0.568 AC: 167 AN: 294

European-Non Finnish (NFE) AF: 0.644 AC: 43689 AN: 67834

Other (OTH) AF: 0.630 AC: 1324 AN: 2102

Alfa AF: 0.649 Hom.: 16548

Bravo AF: 0.673

Asia WGS AF: 0.487 AC: 1694 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.5
DANN	Benign	0.54
PhyloP100		-0.21

Splicing

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

Other links and lift over

dbSNP: rs2685729; hg19: chr2-82187352;