chr14-92292101-G-A

Variant names:

• chr14-92292101-G-A
• rs8016079
• ENST00000826664.1:n.121+4742G>A

Variant summary

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

The ENST00000826664.1(ENSG00000307514):​n.121+4742G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.115 in 152,206 control chromosomes in the GnomAD database, including 1,073 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 0.11 (1073 hom., cov: 32)
• Consequence: ENSG00000307514 ENST00000826664.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.393
• Publications: 3 publications found

Genes affected

ENSG00000307514 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.191 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
ENSG00000307514	ENST00000826664.1	n.121+4742G>A		intron_variant	Intron 1 of 2
ENSG00000307514	ENST00000826665.1	n.116+4742G>A		intron_variant	Intron 1 of 2
ENSG00000307514	ENST00000826666.1	n.112+4742G>A		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.115 AC: 17450 AN: 152086 Hom.: 1071 Cov.: 32

Gnomad AFR AF: 0.0748

Gnomad AMI AF: 0.0439

Gnomad AMR AF: 0.148

Gnomad ASJ AF: 0.0928

Gnomad EAS AF: 0.201

Gnomad SAS AF: 0.128

Gnomad FIN AF: 0.124

Gnomad MID AF: 0.0759

Gnomad NFE AF: 0.125

Gnomad OTH AF: 0.124

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

GnomAD4 genome AF: 0.115 AC: 17462 AN: 152206 Hom.: 1073 Cov.: 32 AF XY: 0.116 AC XY: 8651 AN XY: 74412

African (AFR) AF: 0.0749 AC: 3113 AN: 41542

American (AMR) AF: 0.148 AC: 2265 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.0928 AC: 322 AN: 3468

East Asian (EAS) AF: 0.201 AC: 1041 AN: 5176

South Asian (SAS) AF: 0.128 AC: 617 AN: 4830

European-Finnish (FIN) AF: 0.124 AC: 1314 AN: 10604

Middle Eastern (MID) AF: 0.0680 AC: 20 AN: 294

European-Non Finnish (NFE) AF: 0.125 AC: 8469 AN: 67996

Other (OTH) AF: 0.124 AC: 261 AN: 2108

Alfa AF: 0.124 Hom.: 1078

Bravo AF: 0.117

Asia WGS AF: 0.135 AC: 471 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	2.3
DANN	Benign	0.57
PhyloP100		0.39

Splicing

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

Other links and lift over

dbSNP: rs8016079; hg19: chr14-92758445;