1-86832166-T-C

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 6 publications found

Genes affected

ENSG00000284846 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000646669.1. 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000284846	ENST00000646669.1		n.186+244A>G		intron	N/A

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

African (AFR) AF: 0.132 AC: 5499 AN: 41508

American (AMR) AF: 0.477 AC: 7280 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.446 AC: 1550 AN: 3472

East Asian (EAS) AF: 0.368 AC: 1900 AN: 5168

South Asian (SAS) AF: 0.370 AC: 1786 AN: 4828

European-Finnish (FIN) AF: 0.571 AC: 6023 AN: 10552

Middle Eastern (MID) AF: 0.349 AC: 102 AN: 292

European-Non Finnish (NFE) AF: 0.529 AC: 35954 AN: 67986

Other (OTH) AF: 0.396 AC: 836 AN: 2112

Alfa AF: 0.484 Hom.: 35849

Bravo AF: 0.385

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	3.7
DANN	Benign	0.60
PhyloP100		0.16

Splicing

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

Other links and lift over

dbSNP: rs12142266; hg19: chr1-87297849;