rs1386809

Variant names:

• chr12-55031132-A-C
• rs1386809
• ENST00000781897.1:n.93-1812T>G

Your query was ambiguous. Multiple possible variants found:

• chr12-55031132-A-C
• chr12-55031132-A-G
• chr12-55031132-A-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000781897.1(ENSG00000301788):​n.93-1812T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.451 in 152,090 control chromosomes in the GnomAD database, including 18,340 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 0.45 (18340 hom., cov: 32)
• Consequence: ENSG00000301788 ENST00000781897.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.266
• Publications: 5 publications found

Genes affected

ENSG00000301788 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.736 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC101927484	XR_245987.4	n.461-1812T>G		intron_variant	Intron 2 of 4
LOC101927484	XR_245988.3	n.445-1812T>G		intron_variant	Intron 2 of 5
LOC101927484	XR_944985.1	n.445-1817T>G		intron_variant	Intron 2 of 4
LOC101927484	XR_944986.1	n.322-1812T>G		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000301788	ENST00000781897.1	n.93-1812T>G		intron_variant	Intron 1 of 3
ENSG00000301788	ENST00000781898.1	n.426-1812T>G		intron_variant	Intron 2 of 4
ENSG00000301788	ENST00000781899.1	n.458-1812T>G		intron_variant	Intron 2 of 5

Frequencies

GnomAD3 genomes AF: 0.451 AC: 68522 AN: 151974 Hom.: 18273 Cov.: 32

Gnomad AFR AF: 0.743

Gnomad AMI AF: 0.195

Gnomad AMR AF: 0.476

Gnomad ASJ AF: 0.249

Gnomad EAS AF: 0.387

Gnomad SAS AF: 0.398

Gnomad FIN AF: 0.337

Gnomad MID AF: 0.392

Gnomad NFE AF: 0.309

Gnomad OTH AF: 0.424

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

GnomAD4 genome AF: 0.451 AC: 68655 AN: 152090 Hom.: 18340 Cov.: 32 AF XY: 0.452 AC XY: 33605 AN XY: 74358

African (AFR) AF: 0.743 AC: 30850 AN: 41506

American (AMR) AF: 0.477 AC: 7283 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.249 AC: 862 AN: 3468

East Asian (EAS) AF: 0.387 AC: 2002 AN: 5174

South Asian (SAS) AF: 0.399 AC: 1922 AN: 4820

European-Finnish (FIN) AF: 0.337 AC: 3566 AN: 10580

Middle Eastern (MID) AF: 0.398 AC: 117 AN: 294

European-Non Finnish (NFE) AF: 0.309 AC: 20972 AN: 67956

Other (OTH) AF: 0.428 AC: 904 AN: 2112

Alfa AF: 0.504 Hom.: 9081

Bravo AF: 0.471

Asia WGS AF: 0.441 AC: 1533 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.3
DANN	Benign	0.30
PhyloP100		-0.27

Splicing

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

Other links and lift over

dbSNP: rs1386809; hg19: chr12-55424916;