14-104446873-G-T

Variant names:

• chr14-104446873-G-T
• rs11628179
• ENST00000816898.1:n.119-2038C>A

Variant summary

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

The ENST00000816898.1(ENSG00000306308):​n.119-2038C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.207 in 152,256 control chromosomes in the GnomAD database, including 4,068 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 0.21 (4068 hom., cov: 33)
• Consequence: ENSG00000306308 ENST00000816898.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.86
• Publications: 1 publications found

Genes affected

ENSG00000306308 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.458 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
ENSG00000306308	ENST00000816898.1	n.119-2038C>A		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.207 AC: 31434 AN: 152138 Hom.: 4061 Cov.: 33

Gnomad AFR AF: 0.0924

Gnomad AMI AF: 0.271

Gnomad AMR AF: 0.384

Gnomad ASJ AF: 0.211

Gnomad EAS AF: 0.473

Gnomad SAS AF: 0.306

Gnomad FIN AF: 0.182

Gnomad MID AF: 0.212

Gnomad NFE AF: 0.211

Gnomad OTH AF: 0.226

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

GnomAD4 genome AF: 0.207 AC: 31462 AN: 152256 Hom.: 4068 Cov.: 33 AF XY: 0.211 AC XY: 15722 AN XY: 74434

African (AFR) AF: 0.0924 AC: 3841 AN: 41568

American (AMR) AF: 0.385 AC: 5886 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.211 AC: 734 AN: 3472

East Asian (EAS) AF: 0.474 AC: 2453 AN: 5178

South Asian (SAS) AF: 0.306 AC: 1475 AN: 4826

European-Finnish (FIN) AF: 0.182 AC: 1929 AN: 10602

Middle Eastern (MID) AF: 0.197 AC: 58 AN: 294

European-Non Finnish (NFE) AF: 0.211 AC: 14359 AN: 67992

Other (OTH) AF: 0.227 AC: 480 AN: 2116

Alfa AF: 0.155 Hom.: 457

Bravo AF: 0.220

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.034
DANN	Benign	0.40
PhyloP100		-1.9

Splicing

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

Other links and lift over

dbSNP: rs11628179; hg19: chr14-104913210;