14-56777607-C-T

Variant names:

• chr14-56777607-C-T
• rs12897597
• ENST00000773249.1:n.404+18622G>A

Variant summary

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

The ENST00000773249.1(ENSG00000259133):​n.404+18622G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.2 in 152,088 control chromosomes in the GnomAD database, including 3,390 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 0.20 (3390 hom., cov: 33)
• Consequence: ENSG00000259133 ENST00000773249.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.446
• Publications: 1 publications found

Genes affected

ENSG00000259133 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.266 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000773249.1. 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
	ENSG00000259133	ENST00000773249.1		n.404+18622G>A		intron	N/A
	ENSG00000259133	ENST00000773250.1		n.256+18622G>A		intron	N/A
	ENSG00000259133	ENST00000773251.1		n.469+18622G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.200 AC: 30437 AN: 151970 Hom.: 3387 Cov.: 33

Gnomad AFR AF: 0.241

Gnomad AMI AF: 0.0757

Gnomad AMR AF: 0.273

Gnomad ASJ AF: 0.195

Gnomad EAS AF: 0.165

Gnomad SAS AF: 0.196

Gnomad FIN AF: 0.279

Gnomad MID AF: 0.120

Gnomad NFE AF: 0.153

Gnomad OTH AF: 0.188

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

GnomAD4 genome AF: 0.200 AC: 30460 AN: 152088 Hom.: 3390 Cov.: 33 AF XY: 0.206 AC XY: 15311 AN XY: 74334

African (AFR) AF: 0.241 AC: 9994 AN: 41480

American (AMR) AF: 0.273 AC: 4173 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.195 AC: 675 AN: 3470

East Asian (EAS) AF: 0.164 AC: 848 AN: 5182

South Asian (SAS) AF: 0.194 AC: 936 AN: 4824

European-Finnish (FIN) AF: 0.279 AC: 2943 AN: 10558

Middle Eastern (MID) AF: 0.122 AC: 36 AN: 294

European-Non Finnish (NFE) AF: 0.153 AC: 10394 AN: 67980

Other (OTH) AF: 0.185 AC: 392 AN: 2114

Alfa AF: 0.194 Hom.: 784

Bravo AF: 0.204

Asia WGS AF: 0.198 AC: 690 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	12
DANN	Benign	0.53
PhyloP100		0.45

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: rs12897597;

hg19: chr14-57244325;