14-64896897-A-G

Variant names:

• chr14-64896897-A-G
• rs12881353
• ENST00000797561.1:n.238+5175T>C

Variant summary

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

The ENST00000797561.1(ENSG00000303859):​n.238+5175T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.531 in 104,178 control chromosomes in the GnomAD database, including 21,063 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 0.53 (21063 hom., cov: 26)
• Consequence: ENSG00000303859 ENST00000797561.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00400
• Publications: 5 publications found

Genes affected

ENSG00000303859 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.802 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000797561.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000303859	ENST00000797561.1		n.238+5175T>C		intron	N/A
	ENSG00000303859	ENST00000797562.1		n.221+5175T>C		intron	N/A
	ENSG00000303859	ENST00000797563.1		n.123+5175T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.531 AC: 55300 AN: 104060 Hom.: 21063 Cov.: 26

Gnomad AFR AF: 0.165

Gnomad AMI AF: 0.603

Gnomad AMR AF: 0.684

Gnomad ASJ AF: 0.655

Gnomad EAS AF: 0.300

Gnomad SAS AF: 0.624

Gnomad FIN AF: 0.675

Gnomad MID AF: 0.679

Gnomad NFE AF: 0.809

Gnomad OTH AF: 0.582

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

GnomAD4 genome AF: 0.531 AC: 55307 AN: 104178 Hom.: 21063 Cov.: 26 AF XY: 0.528 AC XY: 26870 AN XY: 50850

African (AFR) AF: 0.164 AC: 5957 AN: 36270

American (AMR) AF: 0.684 AC: 6847 AN: 10014

Ashkenazi Jewish (ASJ) AF: 0.655 AC: 1417 AN: 2164

East Asian (EAS) AF: 0.300 AC: 1212 AN: 4040

South Asian (SAS) AF: 0.626 AC: 2137 AN: 3414

European-Finnish (FIN) AF: 0.675 AC: 4212 AN: 6240

Middle Eastern (MID) AF: 0.657 AC: 130 AN: 198

European-Non Finnish (NFE) AF: 0.809 AC: 32238 AN: 39854

Other (OTH) AF: 0.576 AC: 828 AN: 1438

Alfa AF: 0.619 Hom.: 22679

Bravo AF: 0.562

Asia WGS AF: 0.314 AC: 798 AN: 2540

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	10
DANN	Benign	0.67
PhyloP100		-0.0040

Splicing

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

Other links and lift over

dbSNP: rs12881353; hg19: chr14-65363615;