rs2285211

Positions:

• 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: ENST00000392097.5 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.691

Genes affected

(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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000392097.5	n.6093G>A		non_coding_transcript_exon_variant	1/1

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;