ENST00000789688.1:n.277+16331G>A

Variant names:

• chr12-5138768-G-A
• rs114306
• ENST00000789688.1:n.277+16331G>A

Variant summary

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

The ENST00000789688.1(ENSG00000256417):​n.277+16331G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.255 in 152,026 control chromosomes in the GnomAD database, including 5,313 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 0.26 (5313 hom., cov: 33)
• Consequence: ENSG00000256417 ENST00000789688.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.03
• Publications: 3 publications found

Genes affected

ENSG00000256417 (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 (NFE) allele frequency at 95% confidence interval = 0.307 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000789688.1. 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
	LOC105369617	NR_188065.1		n.538+16284G>A		intron	N/A
	LOC105369617	NR_188066.1		n.521+16301G>A		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000256417	ENST00000789688.1		n.277+16331G>A		intron	N/A
	ENSG00000256417	ENST00000789689.1		n.269+16331G>A		intron	N/A
	ENSG00000256417	ENST00000789690.1		n.255+16331G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.256 AC: 38845 AN: 151908 Hom.: 5321 Cov.: 33

Gnomad AFR AF: 0.194

Gnomad AMI AF: 0.311

Gnomad AMR AF: 0.196

Gnomad ASJ AF: 0.324

Gnomad EAS AF: 0.0478

Gnomad SAS AF: 0.285

Gnomad FIN AF: 0.284

Gnomad MID AF: 0.386

Gnomad NFE AF: 0.311

Gnomad OTH AF: 0.270

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

GnomAD4 genome AF: 0.255 AC: 38830 AN: 152026 Hom.: 5313 Cov.: 33 AF XY: 0.253 AC XY: 18836 AN XY: 74312

African (AFR) AF: 0.193 AC: 8022 AN: 41468

American (AMR) AF: 0.195 AC: 2984 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.324 AC: 1123 AN: 3470

East Asian (EAS) AF: 0.0480 AC: 247 AN: 5150

South Asian (SAS) AF: 0.284 AC: 1367 AN: 4812

European-Finnish (FIN) AF: 0.284 AC: 2997 AN: 10560

Middle Eastern (MID) AF: 0.371 AC: 109 AN: 294

European-Non Finnish (NFE) AF: 0.311 AC: 21135 AN: 67988

Other (OTH) AF: 0.268 AC: 563 AN: 2104

Alfa AF: 0.233 Hom.: 1121

Bravo AF: 0.243

Asia WGS AF: 0.148 AC: 514 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	11
DANN	Benign	0.66
PhyloP100		1.0

Splicing

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

Other links and lift over

dbSNP: rs114306; hg19: chr12-5247934;