rs1894692

Variant names:

• chr1-169498416-G-A
• rs1894692
• ENST00000392097.6:n.12345G>A

Variant summary

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

The ENST00000392097.6(ENSG00000213062):​n.12345G>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 0.984 in 152,178 control chromosomes in the GnomAD database, including 73,746 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 0.98 (73746 hom., cov: 29)
• Consequence: ENSG00000213062 ENST00000392097.6 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.826
• Publications: 14 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=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.988 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

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

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000213062	ENST00000392097.6	TSL:6	n.12345G>A		non_coding_transcript_exon	Exon 1 of 1

Frequencies

GnomAD3 genomes AF: 0.984 AC: 149680 AN: 152060 Hom.: 73684 Cov.: 29

Gnomad AFR AF: 0.996

Gnomad AMI AF: 0.907

Gnomad AMR AF: 0.995

Gnomad ASJ AF: 0.980

Gnomad EAS AF: 1.00

Gnomad SAS AF: 0.995

Gnomad FIN AF: 0.977

Gnomad MID AF: 0.965

Gnomad NFE AF: 0.976

Gnomad OTH AF: 0.984

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

GnomAD4 genome AF: 0.984 AC: 149801 AN: 152178 Hom.: 73746 Cov.: 29 AF XY: 0.985 AC XY: 73293 AN XY: 74404

African (AFR) AF: 0.996 AC: 41331 AN: 41494

American (AMR) AF: 0.995 AC: 15206 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.980 AC: 3401 AN: 3470

East Asian (EAS) AF: 1.00 AC: 5166 AN: 5166

South Asian (SAS) AF: 0.995 AC: 4791 AN: 4814

European-Finnish (FIN) AF: 0.977 AC: 10347 AN: 10596

Middle Eastern (MID) AF: 0.969 AC: 285 AN: 294

European-Non Finnish (NFE) AF: 0.976 AC: 66370 AN: 68034

Other (OTH) AF: 0.984 AC: 2077 AN: 2110

Alfa AF: 0.982 Hom.: 9107

Bravo AF: 0.985

Asia WGS AF: 0.997 AC: 3469 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.98
DANN	Benign	0.50
PhyloP100		-0.83

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs1894692;

hg19: chr1-169467654;