14-64891858-C-T

Variant names:

• chr14-64891858-C-T
• rs1957425
• ENST00000797561.1:n.239-5868G>A

Variant summary

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

The ENST00000797561.1(ENSG00000303859):​n.239-5868G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.582 in 152,176 control chromosomes in the GnomAD database, including 30,407 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 0.58 (30407 hom., cov: 33)
• Consequence: ENSG00000303859 ENST00000797561.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.821
• Publications: 14 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=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.768 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

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
	ENSG00000303859	ENST00000797561.1		n.239-5868G>A		intron	N/A
	ENSG00000303859	ENST00000797562.1		n.222-5868G>A		intron	N/A
	ENSG00000303859	ENST00000797563.1		n.124-5868G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.583 AC: 88614 AN: 152058 Hom.: 30414 Cov.: 33

Gnomad AFR AF: 0.215

Gnomad AMI AF: 0.630

Gnomad AMR AF: 0.694

Gnomad ASJ AF: 0.672

Gnomad EAS AF: 0.363

Gnomad SAS AF: 0.649

Gnomad FIN AF: 0.669

Gnomad MID AF: 0.693

Gnomad NFE AF: 0.773

Gnomad OTH AF: 0.625

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

GnomAD4 genome AF: 0.582 AC: 88614 AN: 152176 Hom.: 30407 Cov.: 33 AF XY: 0.580 AC XY: 43114 AN XY: 74396

African (AFR) AF: 0.215 AC: 8905 AN: 41512

American (AMR) AF: 0.694 AC: 10614 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.672 AC: 2332 AN: 3472

East Asian (EAS) AF: 0.363 AC: 1881 AN: 5178

South Asian (SAS) AF: 0.650 AC: 3135 AN: 4826

European-Finnish (FIN) AF: 0.669 AC: 7090 AN: 10590

Middle Eastern (MID) AF: 0.680 AC: 200 AN: 294

European-Non Finnish (NFE) AF: 0.773 AC: 52574 AN: 67982

Other (OTH) AF: 0.620 AC: 1310 AN: 2112

Alfa AF: 0.721 Hom.: 34205

Bravo AF: 0.562

Asia WGS AF: 0.484 AC: 1683 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	14
DANN	Benign	0.38
PhyloP100		0.82

Splicing

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

Other links and lift over

dbSNP: rs1957425; hg19: chr14-65358576;