chr2-219986453-G-A

Variant names:

• chr2-219986453-G-A
• rs13414052
• ENST00000692185.2:n.279-38180G>A

Variant summary

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

The ENST00000692185.2(ENSG00000288902):​n.279-38180G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.244 in 152,112 control chromosomes in the GnomAD database, including 5,377 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 0.24 (5377 hom., cov: 32)
• Consequence: ENSG00000288902 ENST00000692185.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.32
• Publications: 2 publications found

Genes affected

ENSG00000288902 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.316 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000692185.2. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000288902	ENST00000692185.2		n.279-38180G>A		intron	N/A
	ENSG00000288902	ENST00000702748.2		n.353-38180G>A		intron	N/A
	ENSG00000288902	ENST00000830324.1		n.310-38180G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.244 AC: 37121 AN: 151994 Hom.: 5378 Cov.: 32

Gnomad AFR AF: 0.0887

Gnomad AMI AF: 0.259

Gnomad AMR AF: 0.200

Gnomad ASJ AF: 0.315

Gnomad EAS AF: 0.265

Gnomad SAS AF: 0.316

Gnomad FIN AF: 0.360

Gnomad MID AF: 0.250

Gnomad NFE AF: 0.320

Gnomad OTH AF: 0.260

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

GnomAD4 genome AF: 0.244 AC: 37135 AN: 152112 Hom.: 5377 Cov.: 32 AF XY: 0.247 AC XY: 18354 AN XY: 74362

African (AFR) AF: 0.0887 AC: 3681 AN: 41488

American (AMR) AF: 0.199 AC: 3047 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.315 AC: 1093 AN: 3466

East Asian (EAS) AF: 0.265 AC: 1372 AN: 5184

South Asian (SAS) AF: 0.318 AC: 1534 AN: 4822

European-Finnish (FIN) AF: 0.360 AC: 3811 AN: 10582

Middle Eastern (MID) AF: 0.248 AC: 73 AN: 294

European-Non Finnish (NFE) AF: 0.320 AC: 21741 AN: 67964

Other (OTH) AF: 0.259 AC: 547 AN: 2110

Alfa AF: 0.294 Hom.: 9364

Bravo AF: 0.225

Asia WGS AF: 0.277 AC: 963 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.039
DANN	Benign	0.63
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs13414052; hg19: chr2-220851174;