rs12443878

Variant names:

• chr16-82626328-C-A
• rs12443878
• ENST00000793365.1:n.982G>T

Variant summary

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

The ENST00000793365.1(ENSG00000303284):​n.982G>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.368 in 152,052 control chromosomes in the GnomAD database, including 11,710 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 0.37 (11710 hom., cov: 33)
• Consequence: ENSG00000303284 ENST00000793365.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0920
• Publications: 3 publications found

Genes affected

ENSG00000303284 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.473 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
ENSG00000303284	ENST00000793365.1	n.982G>T		non_coding_transcript_exon_variant	Exon 1 of 2

Frequencies

GnomAD3 genomes AF: 0.368 AC: 55907 AN: 151934 Hom.: 11709 Cov.: 33

Gnomad AFR AF: 0.228

Gnomad AMI AF: 0.541

Gnomad AMR AF: 0.297

Gnomad ASJ AF: 0.419

Gnomad EAS AF: 0.00599

Gnomad SAS AF: 0.357

Gnomad FIN AF: 0.466

Gnomad MID AF: 0.380

Gnomad NFE AF: 0.477

Gnomad OTH AF: 0.358

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

GnomAD4 genome AF: 0.368 AC: 55923 AN: 152052 Hom.: 11710 Cov.: 33 AF XY: 0.365 AC XY: 27099 AN XY: 74324

African (AFR) AF: 0.228 AC: 9462 AN: 41482

American (AMR) AF: 0.297 AC: 4541 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.419 AC: 1452 AN: 3468

East Asian (EAS) AF: 0.00581 AC: 30 AN: 5162

South Asian (SAS) AF: 0.357 AC: 1715 AN: 4806

European-Finnish (FIN) AF: 0.466 AC: 4924 AN: 10564

Middle Eastern (MID) AF: 0.388 AC: 114 AN: 294

European-Non Finnish (NFE) AF: 0.477 AC: 32435 AN: 67962

Other (OTH) AF: 0.359 AC: 757 AN: 2106

Alfa AF: 0.424 Hom.: 18717

Bravo AF: 0.342

Asia WGS AF: 0.193 AC: 673 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	4.9
DANN	Benign	0.60
PhyloP100		-0.092

Splicing

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

Other links and lift over

dbSNP: rs12443878; hg19: chr16-82659933; COSMIC: COSV51819680;