ENST00000681682.2:n.616+14998T>G

Variant names:

• chr4-111132270-T-G
• rs192709
• ENST00000681682.2:n.616+14998T>G

Variant summary

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

The ENST00000681682.2(ENSG00000288692):​n.616+14998T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.361 in 151,994 control chromosomes in the GnomAD database, including 10,413 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 0.36 (10413 hom., cov: 32)
• Consequence: ENSG00000288692 ENST00000681682.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.185
• Publications: 1 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=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.417 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
ENSG00000288692	ENST00000681682.2	n.616+14998T>G		intron_variant	Intron 3 of 5

Frequencies

GnomAD3 genomes AF: 0.361 AC: 54830 AN: 151876 Hom.: 10407 Cov.: 32

Gnomad AFR AF: 0.302

Gnomad AMI AF: 0.218

Gnomad AMR AF: 0.292

Gnomad ASJ AF: 0.291

Gnomad EAS AF: 0.239

Gnomad SAS AF: 0.354

Gnomad FIN AF: 0.414

Gnomad MID AF: 0.225

Gnomad NFE AF: 0.421

Gnomad OTH AF: 0.326

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

GnomAD4 genome AF: 0.361 AC: 54867 AN: 151994 Hom.: 10413 Cov.: 32 AF XY: 0.358 AC XY: 26605 AN XY: 74286

African (AFR) AF: 0.302 AC: 12505 AN: 41424

American (AMR) AF: 0.292 AC: 4460 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.291 AC: 1011 AN: 3470

East Asian (EAS) AF: 0.238 AC: 1233 AN: 5170

South Asian (SAS) AF: 0.354 AC: 1704 AN: 4816

European-Finnish (FIN) AF: 0.414 AC: 4371 AN: 10568

Middle Eastern (MID) AF: 0.218 AC: 64 AN: 294

European-Non Finnish (NFE) AF: 0.421 AC: 28630 AN: 67958

Other (OTH) AF: 0.328 AC: 690 AN: 2106

Alfa AF: 0.388 Hom.: 1514

Bravo AF: 0.347

Asia WGS AF: 0.314 AC: 1094 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.6
DANN	Benign	0.47
PhyloP100		0.18

Splicing

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

Other links and lift over

dbSNP: rs192709; hg19: chr4-112053426;