rs1894691

chr1-169498372-G-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: ENST00000392097.5 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0680

Genes affected

(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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000392097.5	n.12297G>A		non_coding_transcript_exon_variant	1/1

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

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;