chr2-205624359-C-T

Variant names:

• chr2-205624359-C-T
• rs11681709
• ENST00000792092.1:n.579-1204G>A

Variant summary

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

The ENST00000792092.1(ENSG00000303132):​n.579-1204G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.314 in 152,076 control chromosomes in the GnomAD database, including 8,332 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 0.31 (8332 hom., cov: 32)
• Consequence: ENSG00000303132 ENST00000792092.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.798
• Publications: 3 publications found

Genes affected

ENSG00000303132 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.405 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000792092.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000303132	ENST00000792092.1		n.579-1204G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.314 AC: 47745 AN: 151958 Hom.: 8339 Cov.: 32

Gnomad AFR AF: 0.238

Gnomad AMI AF: 0.271

Gnomad AMR AF: 0.283

Gnomad ASJ AF: 0.445

Gnomad EAS AF: 0.00193

Gnomad SAS AF: 0.135

Gnomad FIN AF: 0.223

Gnomad MID AF: 0.478

Gnomad NFE AF: 0.409

Gnomad OTH AF: 0.375

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

GnomAD4 genome AF: 0.314 AC: 47746 AN: 152076 Hom.: 8332 Cov.: 32 AF XY: 0.302 AC XY: 22453 AN XY: 74346

African (AFR) AF: 0.238 AC: 9885 AN: 41478

American (AMR) AF: 0.283 AC: 4323 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.445 AC: 1541 AN: 3464

East Asian (EAS) AF: 0.00193 AC: 10 AN: 5174

South Asian (SAS) AF: 0.135 AC: 649 AN: 4818

European-Finnish (FIN) AF: 0.223 AC: 2363 AN: 10586

Middle Eastern (MID) AF: 0.466 AC: 137 AN: 294

European-Non Finnish (NFE) AF: 0.409 AC: 27811 AN: 67960

Other (OTH) AF: 0.370 AC: 781 AN: 2112

Alfa AF: 0.338 Hom.: 1708

Bravo AF: 0.316

Asia WGS AF: 0.0770 AC: 267 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.7
DANN	Benign	0.86
PhyloP100		-0.80

Splicing

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

Other links and lift over

dbSNP: rs11681709; hg19: chr2-206489083;