rs1994104

Positions:

• chr12-84122733-C-T

Variant summary

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

The ENST00000689302.1(ENSG00000289309):​n.112-61579G>A variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0828 in 152,118 control chromosomes in the GnomAD database, including 711 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 0.083 (711 hom., cov: 32)
• Consequence: ENST00000689302.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.28

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.152 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC107984536	XR_001749235.2	n.112-61579G>A		intron_variant, non_coding_transcript_variant
LOC107984536	XR_001749234.2	n.112-61579G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000689302.1	n.112-61579G>A		intron_variant, non_coding_transcript_variant
	ENST00000688936.2	n.112-61579G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0828 AC: 12589 AN: 152000 Hom.: 710 Cov.: 32

Gnomad AFR AF: 0.155

Gnomad AMI AF: 0.145

Gnomad AMR AF: 0.0541

Gnomad ASJ AF: 0.0438

Gnomad EAS AF: 0.000193

Gnomad SAS AF: 0.0126

Gnomad FIN AF: 0.0466

Gnomad MID AF: 0.0316

Gnomad NFE AF: 0.0636

Gnomad OTH AF: 0.0772

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

GnomAD4 genome AF: 0.0828 AC: 12593 AN: 152118 Hom.: 711 Cov.: 32 AF XY: 0.0777 AC XY: 5778 AN XY: 74390

Gnomad4 AFR AF: 0.155

Gnomad4 AMR AF: 0.0539

Gnomad4 ASJ AF: 0.0438

Gnomad4 EAS AF: 0.000194

Gnomad4 SAS AF: 0.0124

Gnomad4 FIN AF: 0.0466

Gnomad4 NFE AF: 0.0636

Gnomad4 OTH AF: 0.0764

Alfa AF: 0.0688 Hom.: 390

Bravo AF: 0.0874

Asia WGS AF: 0.0150 AC: 53 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.25
DANN	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1994104; hg19: chr12-84516512;