chr14-76654401-T-C

Variant names:

• chr14-76654401-T-C
• rs11159221
• ENST00000554926.1:n.195-52809A>G

Variant summary

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

The ENST00000554926.1(ENSG00000259124):​n.195-52809A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.189 in 152,178 control chromosomes in the GnomAD database, including 2,847 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 0.19 (2847 hom., cov: 32)
• Consequence: ENSG00000259124 ENST00000554926.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.852
• Publications: 6 publications found

Genes affected

ENSG00000259124 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.238 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000554926.1. 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
	ENSG00000259124	ENST00000554926.1	TSL:3	n.195-52809A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.189 AC: 28807 AN: 152060 Hom.: 2841 Cov.: 32

Gnomad AFR AF: 0.241

Gnomad AMI AF: 0.149

Gnomad AMR AF: 0.132

Gnomad ASJ AF: 0.145

Gnomad EAS AF: 0.205

Gnomad SAS AF: 0.164

Gnomad FIN AF: 0.168

Gnomad MID AF: 0.215

Gnomad NFE AF: 0.177

Gnomad OTH AF: 0.185

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

GnomAD4 genome AF: 0.189 AC: 28835 AN: 152178 Hom.: 2847 Cov.: 32 AF XY: 0.187 AC XY: 13939 AN XY: 74400

African (AFR) AF: 0.242 AC: 10028 AN: 41512

American (AMR) AF: 0.132 AC: 2017 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.145 AC: 502 AN: 3466

East Asian (EAS) AF: 0.205 AC: 1057 AN: 5162

South Asian (SAS) AF: 0.164 AC: 790 AN: 4828

European-Finnish (FIN) AF: 0.168 AC: 1777 AN: 10600

Middle Eastern (MID) AF: 0.214 AC: 63 AN: 294

European-Non Finnish (NFE) AF: 0.177 AC: 12065 AN: 67998

Other (OTH) AF: 0.189 AC: 400 AN: 2114

Alfa AF: 0.182 Hom.: 10256

Bravo AF: 0.192

Asia WGS AF: 0.178 AC: 620 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	6.6
DANN	Benign	0.43
PhyloP100		0.85

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: rs11159221;

hg19: chr14-77120744;