chr2-210267691-A-G

Variant names:

• chr2-210267691-A-G
• rs1509569
• ENST00000795993.1:n.270-12052A>G

Variant summary

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

The ENST00000795993.1(ENSG00000279317):​n.270-12052A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.412 in 152,050 control chromosomes in the GnomAD database, including 13,100 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 0.41 (13100 hom., cov: 32)
• Consequence: ENSG00000279317 ENST00000795993.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.771
• Publications: 13 publications found

Genes affected

ENSG00000279317 (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 (EAS) allele frequency at 95% confidence interval = 0.473 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
ENSG00000279317	ENST00000795993.1	n.270-12052A>G		intron_variant	Intron 3 of 5

Frequencies

GnomAD3 genomes AF: 0.412 AC: 62621 AN: 151932 Hom.: 13099 Cov.: 32

Gnomad AFR AF: 0.378

Gnomad AMI AF: 0.423

Gnomad AMR AF: 0.333

Gnomad ASJ AF: 0.375

Gnomad EAS AF: 0.488

Gnomad SAS AF: 0.371

Gnomad FIN AF: 0.472

Gnomad MID AF: 0.294

Gnomad NFE AF: 0.441

Gnomad OTH AF: 0.396

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

GnomAD4 genome AF: 0.412 AC: 62621 AN: 152050 Hom.: 13100 Cov.: 32 AF XY: 0.410 AC XY: 30488 AN XY: 74310

African (AFR) AF: 0.377 AC: 15650 AN: 41468

American (AMR) AF: 0.332 AC: 5069 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.375 AC: 1302 AN: 3472

East Asian (EAS) AF: 0.488 AC: 2529 AN: 5178

South Asian (SAS) AF: 0.369 AC: 1783 AN: 4828

European-Finnish (FIN) AF: 0.472 AC: 4990 AN: 10572

Middle Eastern (MID) AF: 0.282 AC: 83 AN: 294

European-Non Finnish (NFE) AF: 0.441 AC: 29989 AN: 67954

Other (OTH) AF: 0.397 AC: 840 AN: 2116

Alfa AF: 0.430 Hom.: 61364

Bravo AF: 0.403

Asia WGS AF: 0.400 AC: 1388 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	9.1
DANN	Benign	0.74
PhyloP100		0.77

Splicing

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

Other links and lift over

dbSNP: rs1509569; hg19: chr2-211132415;