rs13414052

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105373891	XR_001739888.2	n.304-27317G>A		intron_variant	Intron 1 of 4
LOC105373891	XR_923928.3	n.124+25670G>A		intron_variant	Intron 1 of 4
LOC105373891	XR_923930.3	n.124+25670G>A		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000288902	ENST00000692185.2	n.279-38180G>A		intron_variant	Intron 1 of 3
ENSG00000288902	ENST00000702748.2	n.353-38180G>A		intron_variant	Intron 1 of 3
ENSG00000288902	ENST00000830324.1	n.310-38180G>A		intron_variant	Intron 1 of 5

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 v4.3

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;