1-169498372-G-A

Variant names:

• chr1-169498372-G-A
• rs1894691
• ENST00000392097.6:n.12301G>A

Variant summary

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

The ENST00000392097.6(ENSG00000213062):​n.12301G>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 ENST00000392097.6 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0680
• Publications: 1 publications found

Genes affected

ENSG00000213062 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.0961 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000392097.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000213062	ENST00000392097.6	TSL:6	n.12301G>A		non_coding_transcript_exon	Exon 1 of 1

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

African (AFR) AF: 0.0117 AC: 485 AN: 41520

American (AMR) AF: 0.100 AC: 1533 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.0784 AC: 272 AN: 3470

East Asian (EAS) AF: 0.0246 AC: 127 AN: 5168

South Asian (SAS) AF: 0.0749 AC: 361 AN: 4818

European-Finnish (FIN) AF: 0.0848 AC: 899 AN: 10604

Middle Eastern (MID) AF: 0.0850 AC: 25 AN: 294

European-Non Finnish (NFE) AF: 0.0748 AC: 5088 AN: 68004

Other (OTH) AF: 0.0659 AC: 139 AN: 2108

Alfa AF: 0.0705 Hom.: 218

Bravo AF: 0.0542

Asia WGS AF: 0.0570 AC: 201 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.5
DANN	Benign	0.18
PhyloP100		0.068

Splicing

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

Other links and lift over

dbSNP: rs1894691; hg19: chr1-169467610;