rs2285211

Variant names:

• chr1-169492168-G-A
• rs2285211
• ENST00000392097.5:n.6093G>A

Your query was ambiguous. Multiple possible variants found:

• chr1-169492168-G-A
• chr1-169492168-G-C
• chr1-169492168-G-T

Variant summary

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

The ENST00000392097.5(ENSG00000213062):​n.6093G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.441 in 152,024 control chromosomes in the GnomAD database, including 15,781 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 0.44 (15781 hom., cov: 32)
• Consequence: ENSG00000213062 ENST00000392097.5 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.691

Genes affected

ENSG00000213062 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.74).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.535 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000213062	ENST00000392097.5	n.6093G>A		non_coding_transcript_exon_variant	Exon 1 of 1	6

Frequencies

GnomAD3 genomes AF: 0.441 AC: 66946 AN: 151906 Hom.: 15761 Cov.: 32

Gnomad AFR AF: 0.312

Gnomad AMI AF: 0.535

Gnomad AMR AF: 0.420

Gnomad ASJ AF: 0.476

Gnomad EAS AF: 0.152

Gnomad SAS AF: 0.318

Gnomad FIN AF: 0.517

Gnomad MID AF: 0.415

Gnomad NFE AF: 0.539

Gnomad OTH AF: 0.444

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

GnomAD4 genome AF: 0.441 AC: 67005 AN: 152024 Hom.: 15781 Cov.: 32 AF XY: 0.432 AC XY: 32134 AN XY: 74318

Gnomad4 AFR AF: 0.313

Gnomad4 AMR AF: 0.420

Gnomad4 ASJ AF: 0.476

Gnomad4 EAS AF: 0.152

Gnomad4 SAS AF: 0.320

Gnomad4 FIN AF: 0.517

Gnomad4 NFE AF: 0.539

Gnomad4 OTH AF: 0.439

Alfa AF: 0.508 Hom.: 27539

Bravo AF: 0.433

Asia WGS AF: 0.251 AC: 873 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.74
CADD	Benign	7.6
DANN	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2285211; hg19: chr1-169461406;