14-104810872-G-A

Variant names:

• chr14-104810872-G-A
• rs4983559
• ENST00000803113.1:n.318-1313C>T

Variant summary

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

The ENST00000803113.1(ENSG00000279140):​n.318-1313C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.524 in 151,282 control chromosomes in the GnomAD database, including 21,697 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 0.52 (21697 hom., cov: 29)
• Consequence: ENSG00000279140 ENST00000803113.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.262
• Publications: 90 publications found

Genes affected

ENSG00000279140 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.603 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000803113.1. 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
	ENSG00000279140	ENST00000803113.1		n.318-1313C>T		intron	N/A
	ENSG00000279140	ENST00000803114.1		n.292-1310C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.524 AC: 79237 AN: 151164 Hom.: 21671 Cov.: 29

Gnomad AFR AF: 0.410

Gnomad AMI AF: 0.614

Gnomad AMR AF: 0.534

Gnomad ASJ AF: 0.627

Gnomad EAS AF: 0.161

Gnomad SAS AF: 0.424

Gnomad FIN AF: 0.588

Gnomad MID AF: 0.615

Gnomad NFE AF: 0.608

Gnomad OTH AF: 0.544

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

GnomAD4 genome AF: 0.524 AC: 79306 AN: 151282 Hom.: 21697 Cov.: 29 AF XY: 0.519 AC XY: 38316 AN XY: 73838

African (AFR) AF: 0.410 AC: 16894 AN: 41172

American (AMR) AF: 0.534 AC: 8095 AN: 15154

Ashkenazi Jewish (ASJ) AF: 0.627 AC: 2175 AN: 3468

East Asian (EAS) AF: 0.161 AC: 821 AN: 5094

South Asian (SAS) AF: 0.424 AC: 2029 AN: 4786

European-Finnish (FIN) AF: 0.588 AC: 6114 AN: 10404

Middle Eastern (MID) AF: 0.606 AC: 177 AN: 292

European-Non Finnish (NFE) AF: 0.608 AC: 41315 AN: 67912

Other (OTH) AF: 0.539 AC: 1126 AN: 2088

Alfa AF: 0.577 Hom.: 111000

Bravo AF: 0.514

Asia WGS AF: 0.313 AC: 1092 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.0
DANN	Benign	0.32
PhyloP100		-0.26

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: rs4983559;

hg19: chr14-105277209;