rs2037892

Variant names:

• chr2-122370213-G-A
• rs2037892
• ENST00000657880.2:n.755+149294G>A

Your query was ambiguous. Multiple possible variants found:

• chr2-122370213-G-A
• chr2-122370213-G-C
• chr2-122370213-G-T

Variant summary

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

The ENST00000657880.2(ENSG00000286481):​n.755+149294G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.192 in 152,142 control chromosomes in the GnomAD database, including 3,570 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 0.19 (3570 hom., cov: 33)
• Consequence: ENSG00000286481 ENST00000657880.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0480
• Publications: 5 publications found

Genes affected

ENSG00000286481 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.445 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105373592	XR_001739684.2	n.753-22750G>A		intron_variant	Intron 3 of 6
LOC105373592	XR_007087222.1	n.753-22750G>A		intron_variant	Intron 3 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000286481	ENST00000657880.2	n.755+149294G>A		intron_variant	Intron 3 of 8
ENSG00000286481	ENST00000819524.1	n.102-22750G>A		intron_variant	Intron 1 of 2
ENSG00000286481	ENST00000819525.1	n.168+18242G>A		intron_variant	Intron 1 of 2
ENSG00000286481	ENST00000819526.1	n.121+18242G>A		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.192 AC: 29153 AN: 152024 Hom.: 3545 Cov.: 33

Gnomad AFR AF: 0.281

Gnomad AMI AF: 0.144

Gnomad AMR AF: 0.257

Gnomad ASJ AF: 0.186

Gnomad EAS AF: 0.460

Gnomad SAS AF: 0.227

Gnomad FIN AF: 0.126

Gnomad MID AF: 0.165

Gnomad NFE AF: 0.111

Gnomad OTH AF: 0.184

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

GnomAD4 genome AF: 0.192 AC: 29232 AN: 152142 Hom.: 3570 Cov.: 33 AF XY: 0.195 AC XY: 14497 AN XY: 74370

African (AFR) AF: 0.281 AC: 11680 AN: 41494

American (AMR) AF: 0.258 AC: 3945 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.186 AC: 645 AN: 3468

East Asian (EAS) AF: 0.460 AC: 2371 AN: 5152

South Asian (SAS) AF: 0.227 AC: 1093 AN: 4818

European-Finnish (FIN) AF: 0.126 AC: 1338 AN: 10592

Middle Eastern (MID) AF: 0.170 AC: 50 AN: 294

European-Non Finnish (NFE) AF: 0.111 AC: 7578 AN: 68006

Other (OTH) AF: 0.190 AC: 401 AN: 2108

Alfa AF: 0.156 Hom.: 3977

Bravo AF: 0.210

Asia WGS AF: 0.368 AC: 1279 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	4.6
DANN	Benign	0.67
PhyloP100		0.048

Splicing

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

Other links and lift over

dbSNP: rs2037892; hg19: chr2-123127789;