rs2037892

Positions:

• chr2-122370213-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000657880.1(ENSG00000286481):​n.704+149294G>A variant causes a intron, non coding transcript 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: ENST00000657880.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0480

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
LOC105373592	XR_001739684.2	n.753-22750G>A		intron_variant, non_coding_transcript_variant
LOC105373592	XR_007087222.1	n.753-22750G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000657880.1	n.704+149294G>A		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.281

Gnomad4 AMR AF: 0.258

Gnomad4 ASJ AF: 0.186

Gnomad4 EAS AF: 0.460

Gnomad4 SAS AF: 0.227

Gnomad4 FIN AF: 0.126

Gnomad4 NFE AF: 0.111

Gnomad4 OTH AF: 0.190

Alfa AF: 0.159 Hom.: 399

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2037892; hg19: chr2-123127789;