ENST00000681682.2:n.494-85036A>C

Variant names:

• chr4-111032114-A-C
• rs1386389
• ENST00000681682.2:n.494-85036A>C

Variant summary

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

The ENST00000681682.2(ENSG00000288692):​n.494-85036A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.309 in 151,226 control chromosomes in the GnomAD database, including 7,592 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 0.31 (7592 hom., cov: 31)
• Consequence: ENSG00000288692 ENST00000681682.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.51
• Publications: 5 publications found

Genes affected

ENSG00000288692 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.442 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000681682.2. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000288692	ENST00000681682.2		n.494-85036A>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.309 AC: 46678 AN: 151106 Hom.: 7565 Cov.: 31

Gnomad AFR AF: 0.396

Gnomad AMI AF: 0.336

Gnomad AMR AF: 0.318

Gnomad ASJ AF: 0.138

Gnomad EAS AF: 0.458

Gnomad SAS AF: 0.283

Gnomad FIN AF: 0.270

Gnomad MID AF: 0.217

Gnomad NFE AF: 0.259

Gnomad OTH AF: 0.297

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

GnomAD4 genome AF: 0.309 AC: 46752 AN: 151226 Hom.: 7592 Cov.: 31 AF XY: 0.308 AC XY: 22745 AN XY: 73860

African (AFR) AF: 0.396 AC: 16375 AN: 41342

American (AMR) AF: 0.319 AC: 4822 AN: 15138

Ashkenazi Jewish (ASJ) AF: 0.138 AC: 476 AN: 3446

East Asian (EAS) AF: 0.457 AC: 2323 AN: 5078

South Asian (SAS) AF: 0.285 AC: 1369 AN: 4806

European-Finnish (FIN) AF: 0.270 AC: 2851 AN: 10554

Middle Eastern (MID) AF: 0.211 AC: 62 AN: 294

European-Non Finnish (NFE) AF: 0.259 AC: 17532 AN: 67562

Other (OTH) AF: 0.304 AC: 636 AN: 2094

Alfa AF: 0.271 Hom.: 9653

Bravo AF: 0.321

Asia WGS AF: 0.382 AC: 1324 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	5.8
DANN	Benign	0.65
PhyloP100		2.5

Splicing

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

Other links and lift over

dbSNP: rs1386389; hg19: chr4-111953270;