chr1-86832166-T-C

Variant names:

• chr1-86832166-T-C
• rs12142266
• ENST00000646669.1:n.186+244A>G

Variant summary

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

The ENST00000646669.1(ENSG00000284846):​n.186+244A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.403 in 152,092 control chromosomes in the GnomAD database, including 14,749 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 0.40 (14749 hom., cov: 32)
• Consequence: ENSG00000284846 ENST00000646669.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.164

Genes affected

ENSG00000284846 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.524 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
ENSG00000284846	ENST00000646669.1	n.186+244A>G		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.403 AC: 61300 AN: 151974 Hom.: 14754 Cov.: 32

Gnomad AFR AF: 0.133

Gnomad AMI AF: 0.396

Gnomad AMR AF: 0.477

Gnomad ASJ AF: 0.446

Gnomad EAS AF: 0.369

Gnomad SAS AF: 0.370

Gnomad FIN AF: 0.571

Gnomad MID AF: 0.347

Gnomad NFE AF: 0.529

Gnomad OTH AF: 0.398

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

GnomAD4 genome AF: 0.403 AC: 61290 AN: 152092 Hom.: 14749 Cov.: 32 AF XY: 0.405 AC XY: 30118 AN XY: 74328

Gnomad4 AFR AF: 0.132

Gnomad4 AMR AF: 0.477

Gnomad4 ASJ AF: 0.446

Gnomad4 EAS AF: 0.368

Gnomad4 SAS AF: 0.370

Gnomad4 FIN AF: 0.571

Gnomad4 NFE AF: 0.529

Gnomad4 OTH AF: 0.396

Alfa AF: 0.490 Hom.: 26209

Bravo AF: 0.385

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	3.7
DANN	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12142266; hg19: chr1-87297849;