chr14-99275850-T-C

Variant names:

• chr14-99275850-T-C
• rs2664299
• ENST00000742785.1:n.79-168T>C

Variant summary

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

The ENST00000742785.1(ENSG00000296828):​n.79-168T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.291 in 152,110 control chromosomes in the GnomAD database, including 7,992 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 0.29 (7992 hom., cov: 33)
• Consequence: ENSG00000296828 ENST00000742785.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.231
• Publications: 8 publications found

Genes affected

ENSG00000296828 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.58).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.408 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
ENSG00000296828	ENST00000742785.1	n.79-168T>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.292 AC: 44314 AN: 151992 Hom.: 7995 Cov.: 33

Gnomad AFR AF: 0.106

Gnomad AMI AF: 0.395

Gnomad AMR AF: 0.248

Gnomad ASJ AF: 0.340

Gnomad EAS AF: 0.0510

Gnomad SAS AF: 0.200

Gnomad FIN AF: 0.448

Gnomad MID AF: 0.237

Gnomad NFE AF: 0.412

Gnomad OTH AF: 0.286

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

GnomAD4 genome AF: 0.291 AC: 44314 AN: 152110 Hom.: 7992 Cov.: 33 AF XY: 0.287 AC XY: 21353 AN XY: 74352

African (AFR) AF: 0.106 AC: 4392 AN: 41524

American (AMR) AF: 0.248 AC: 3785 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.340 AC: 1177 AN: 3462

East Asian (EAS) AF: 0.0507 AC: 263 AN: 5186

South Asian (SAS) AF: 0.199 AC: 957 AN: 4814

European-Finnish (FIN) AF: 0.448 AC: 4731 AN: 10562

Middle Eastern (MID) AF: 0.235 AC: 69 AN: 294

European-Non Finnish (NFE) AF: 0.412 AC: 27980 AN: 67960

Other (OTH) AF: 0.285 AC: 601 AN: 2108

Alfa AF: 0.371 Hom.: 26602

Bravo AF: 0.270

Asia WGS AF: 0.106 AC: 369 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.58
CADD	Benign	13
DANN	Benign	0.75
PhyloP100		0.23

Splicing

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

Other links and lift over

dbSNP: rs2664299; hg19: chr14-99742187;