chr1-169492168-G-A

Variant names:

• chr1-169492168-G-A
• rs2285211
• ENST00000392097.6:n.6097G>A

Variant summary

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

The ENST00000392097.6(ENSG00000213062):​n.6097G>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 ENST00000392097.6 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.691

Genes affected

ENSG00000213062 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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	ENST00000392097.6	n.6097G>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

African (AFR) AF: 0.313 AC: 12959 AN: 41446

American (AMR) AF: 0.420 AC: 6425 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.476 AC: 1651 AN: 3470

East Asian (EAS) AF: 0.152 AC: 785 AN: 5172

South Asian (SAS) AF: 0.320 AC: 1538 AN: 4810

European-Finnish (FIN) AF: 0.517 AC: 5456 AN: 10562

Middle Eastern (MID) AF: 0.422 AC: 124 AN: 294

European-Non Finnish (NFE) AF: 0.539 AC: 36652 AN: 67964

Other (OTH) AF: 0.439 AC: 928 AN: 2112

Alfa AF: 0.510 Hom.: 37042

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
PhyloP100		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;