14-97383563-G-A

Variant names:

• chr14-97383563-G-A
• rs17095330
• ENST00000846957.1:n.388-125C>T

Variant summary

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

The ENST00000846957.1(ENSG00000310069):​n.388-125C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.256 in 152,078 control chromosomes in the GnomAD database, including 5,070 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 0.26 (5070 hom., cov: 32)
• Consequence: ENSG00000310069 ENST00000846957.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.35
• Publications: 2 publications found

Genes affected

ENSG00000310069 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.293 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000846957.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000310069	ENST00000846957.1		n.388-125C>T		intron	N/A
	ENSG00000310069	ENST00000846959.1		n.185-125C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.256 AC: 38906 AN: 151960 Hom.: 5058 Cov.: 32

Gnomad AFR AF: 0.297

Gnomad AMI AF: 0.297

Gnomad AMR AF: 0.245

Gnomad ASJ AF: 0.351

Gnomad EAS AF: 0.162

Gnomad SAS AF: 0.305

Gnomad FIN AF: 0.181

Gnomad MID AF: 0.377

Gnomad NFE AF: 0.242

Gnomad OTH AF: 0.290

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

GnomAD4 genome AF: 0.256 AC: 38970 AN: 152078 Hom.: 5070 Cov.: 32 AF XY: 0.254 AC XY: 18858 AN XY: 74310

African (AFR) AF: 0.297 AC: 12331 AN: 41462

American (AMR) AF: 0.246 AC: 3755 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.351 AC: 1219 AN: 3470

East Asian (EAS) AF: 0.162 AC: 837 AN: 5176

South Asian (SAS) AF: 0.305 AC: 1471 AN: 4820

European-Finnish (FIN) AF: 0.181 AC: 1916 AN: 10570

Middle Eastern (MID) AF: 0.381 AC: 112 AN: 294

European-Non Finnish (NFE) AF: 0.242 AC: 16449 AN: 67980

Other (OTH) AF: 0.288 AC: 609 AN: 2112

Alfa AF: 0.243 Hom.: 711

Bravo AF: 0.259

Asia WGS AF: 0.237 AC: 820 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.5
DANN	Benign	0.62
PhyloP100		1.3

Splicing

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

Other links and lift over

dbSNP: rs17095330; hg19: chr14-97849900;