rs12132666

Variant names:

• chr1-171378567-G-A
• rs12132666
• ENST00000785012.1:n.306+2377C>T

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BP4_Strong BS2

The ENST00000785012.1(ENSG00000302209):​n.306+2377C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0256 in 149,662 control chromosomes in the GnomAD database, including 91 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 0.026 (91 hom., cov: 27)
• Consequence: ENSG00000302209 ENST00000785012.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0640
• Publications: 1 publications found

Genes affected

ENSG00000302209 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -8 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BS2: High Homozygotes in GnomAd4 at 91 gene

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000785012.1. 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
	ENSG00000302209	ENST00000785012.1		n.306+2377C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0254 AC: 3806 AN: 149556 Hom.: 91 Cov.: 27

Gnomad AFR AF: 0.0703

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.0106

Gnomad ASJ AF: 0.00321

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.0175

Gnomad FIN AF: 0.00875

Gnomad MID AF: 0.00641

Gnomad NFE AF: 0.00923

Gnomad OTH AF: 0.0196

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

GnomAD4 genome AF: 0.0256 AC: 3829 AN: 149662 Hom.: 91 Cov.: 27 AF XY: 0.0245 AC XY: 1789 AN XY: 73062

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5.

African (AFR) AF: 0.0707 AC: 2814 AN: 39814

American (AMR) AF: 0.0106 AC: 160 AN: 15130

Ashkenazi Jewish (ASJ) AF: 0.00321 AC: 11 AN: 3432

East Asian (EAS) AF: 0.00 AC: 0 AN: 5160

South Asian (SAS) AF: 0.0178 AC: 84 AN: 4726

European-Finnish (FIN) AF: 0.00875 AC: 92 AN: 10510

Middle Eastern (MID) AF: 0.0103 AC: 3 AN: 290

European-Non Finnish (NFE) AF: 0.00923 AC: 624 AN: 67626

Other (OTH) AF: 0.0194 AC: 40 AN: 2062

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5. (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.

Alfa AF: 0.0233 Hom.: 12

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.1
DANN	Benign	0.47
PhyloP100		0.064

Splicing

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

Other links and lift over

dbSNP: rs12132666; hg19: chr1-171347706;