ENST00000819868.1:n.84-12697C>T

Variant names:

• chr4-119649267-G-A
• rs2389886
• ENST00000819868.1:n.84-12697C>T

Variant summary

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

The ENST00000819868.1(ENSG00000306632):​n.84-12697C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.245 in 151,932 control chromosomes in the GnomAD database, including 5,000 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 0.24 (5000 hom., cov: 32)
• Consequence: ENSG00000306632 ENST00000819868.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.694
• Publications: 7 publications found

Genes affected

ENSG00000306632 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.397 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
ENSG00000306632	ENST00000819868.1	n.84-12697C>T		intron_variant	Intron 1 of 1
ENSG00000306632	ENST00000819869.1	n.84+7851C>T		intron_variant	Intron 1 of 1
ENSG00000306632	ENST00000819870.1	n.307+7605C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.245 AC: 37162 AN: 151814 Hom.: 4995 Cov.: 32

Gnomad AFR AF: 0.138

Gnomad AMI AF: 0.254

Gnomad AMR AF: 0.319

Gnomad ASJ AF: 0.219

Gnomad EAS AF: 0.412

Gnomad SAS AF: 0.170

Gnomad FIN AF: 0.247

Gnomad MID AF: 0.193

Gnomad NFE AF: 0.286

Gnomad OTH AF: 0.265

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

GnomAD4 genome AF: 0.245 AC: 37175 AN: 151932 Hom.: 5000 Cov.: 32 AF XY: 0.243 AC XY: 18024 AN XY: 74224

African (AFR) AF: 0.137 AC: 5698 AN: 41446

American (AMR) AF: 0.320 AC: 4873 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.219 AC: 761 AN: 3472

East Asian (EAS) AF: 0.412 AC: 2119 AN: 5144

South Asian (SAS) AF: 0.170 AC: 817 AN: 4820

European-Finnish (FIN) AF: 0.247 AC: 2609 AN: 10564

Middle Eastern (MID) AF: 0.194 AC: 57 AN: 294

European-Non Finnish (NFE) AF: 0.286 AC: 19451 AN: 67926

Other (OTH) AF: 0.264 AC: 559 AN: 2114

Alfa AF: 0.257 Hom.: 971

Bravo AF: 0.252

Asia WGS AF: 0.260 AC: 905 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.15
DANN	Benign	0.82
PhyloP100		-0.69

Splicing

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

Other links and lift over

dbSNP: rs2389886; hg19: chr4-120570422;