rs1894691

Variant names:

• chr1-169498372-G-A
• rs1894691
• ENST00000392097.5:n.12297G>A

Variant summary

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

The ENST00000392097.5(ENSG00000213062):​n.12297G>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 0.0589 in 152,186 control chromosomes in the GnomAD database, including 384 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 0.059 (384 hom., cov: 32)
• Consequence: ENSG00000213062 ENST00000392097.5 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0680

Genes affected

ENSG00000213062 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.0961 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.12297G>A		non_coding_transcript_exon_variant	Exon 1 of 1	6

Frequencies

GnomAD3 genomes AF: 0.0590 AC: 8968 AN: 152070 Hom.: 383 Cov.: 32

Gnomad AFR AF: 0.0117

Gnomad AMI AF: 0.0384

Gnomad AMR AF: 0.100

Gnomad ASJ AF: 0.0784

Gnomad EAS AF: 0.0247

Gnomad SAS AF: 0.0753

Gnomad FIN AF: 0.0848

Gnomad MID AF: 0.0886

Gnomad NFE AF: 0.0748

Gnomad OTH AF: 0.0666

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

GnomAD4 genome AF: 0.0589 AC: 8964 AN: 152186 Hom.: 384 Cov.: 32 AF XY: 0.0615 AC XY: 4578 AN XY: 74404

Gnomad4 AFR AF: 0.0117

Gnomad4 AMR AF: 0.100

Gnomad4 ASJ AF: 0.0784

Gnomad4 EAS AF: 0.0246

Gnomad4 SAS AF: 0.0749

Gnomad4 FIN AF: 0.0848

Gnomad4 NFE AF: 0.0748

Gnomad4 OTH AF: 0.0659

Alfa AF: 0.0711 Hom.: 205

Bravo AF: 0.0542

Asia WGS AF: 0.0570 AC: 201 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.5
DANN	Benign	0.18

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1894691; hg19: chr1-169467610;