14-92302159-C-T

Variant names:

• chr14-92302159-C-T
• rs4904866
• ENST00000826664.1:n.122-2249C>T

Variant summary

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

The ENST00000826664.1(ENSG00000307514):​n.122-2249C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.317 in 151,850 control chromosomes in the GnomAD database, including 9,608 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 0.32 (9608 hom., cov: 30)
• Consequence: ENSG00000307514 ENST00000826664.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.320
• Publications: 7 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=-0.8).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.436 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000826664.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000307514	ENST00000826664.1		n.122-2249C>T		intron	N/A
	ENSG00000307514	ENST00000826665.1		n.117-2249C>T		intron	N/A
	ENSG00000307514	ENST00000826666.1		n.113-2249C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.318 AC: 48200 AN: 151732 Hom.: 9604 Cov.: 30

Gnomad AFR AF: 0.0834

Gnomad AMI AF: 0.585

Gnomad AMR AF: 0.287

Gnomad ASJ AF: 0.351

Gnomad EAS AF: 0.345

Gnomad SAS AF: 0.303

Gnomad FIN AF: 0.460

Gnomad MID AF: 0.234

Gnomad NFE AF: 0.440

Gnomad OTH AF: 0.291

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

GnomAD4 genome AF: 0.317 AC: 48206 AN: 151850 Hom.: 9608 Cov.: 30 AF XY: 0.317 AC XY: 23530 AN XY: 74188

African (AFR) AF: 0.0833 AC: 3451 AN: 41436

American (AMR) AF: 0.287 AC: 4374 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.351 AC: 1219 AN: 3468

East Asian (EAS) AF: 0.344 AC: 1772 AN: 5150

South Asian (SAS) AF: 0.303 AC: 1458 AN: 4814

European-Finnish (FIN) AF: 0.460 AC: 4828 AN: 10498

Middle Eastern (MID) AF: 0.231 AC: 68 AN: 294

European-Non Finnish (NFE) AF: 0.440 AC: 29883 AN: 67930

Other (OTH) AF: 0.295 AC: 621 AN: 2102

Alfa AF: 0.389 Hom.: 7468

Bravo AF: 0.292

Asia WGS AF: 0.324 AC: 1126 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	7.8
DANN	Benign	0.70
PhyloP100		0.32

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs4904866;

hg19: chr14-92768503;