rs2402446

Variant names:

• chr14-94399800-T-A
• rs2402446
• ENST00000693506.1:n.124+8906T>A

Variant summary

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

The ENST00000693506.1(ENSG00000256357):​n.124+8906T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.634 in 152,088 control chromosomes in the GnomAD database, including 31,826 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 0.63 (31826 hom., cov: 33)
• Consequence: ENSG00000256357 ENST00000693506.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.717
• Publications: 9 publications found

Genes affected

ENSG00000256357 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.813 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000693506.1. 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
	ENSG00000256357	ENST00000693506.1		n.124+8906T>A		intron	N/A
	ENSG00000256357	ENST00000811346.1		n.227+9935T>A		intron	N/A
	ENSG00000256357	ENST00000811347.1		n.208+9935T>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.634 AC: 96351 AN: 151970 Hom.: 31785 Cov.: 33

Gnomad AFR AF: 0.820

Gnomad AMI AF: 0.571

Gnomad AMR AF: 0.572

Gnomad ASJ AF: 0.633

Gnomad EAS AF: 0.609

Gnomad SAS AF: 0.722

Gnomad FIN AF: 0.562

Gnomad MID AF: 0.554

Gnomad NFE AF: 0.543

Gnomad OTH AF: 0.627

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

GnomAD4 genome AF: 0.634 AC: 96448 AN: 152088 Hom.: 31826 Cov.: 33 AF XY: 0.636 AC XY: 47249 AN XY: 74344

African (AFR) AF: 0.820 AC: 34023 AN: 41496

American (AMR) AF: 0.572 AC: 8745 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.633 AC: 2198 AN: 3472

East Asian (EAS) AF: 0.610 AC: 3150 AN: 5168

South Asian (SAS) AF: 0.723 AC: 3484 AN: 4822

European-Finnish (FIN) AF: 0.562 AC: 5937 AN: 10564

Middle Eastern (MID) AF: 0.554 AC: 163 AN: 294

European-Non Finnish (NFE) AF: 0.543 AC: 36906 AN: 67974

Other (OTH) AF: 0.629 AC: 1325 AN: 2106

Alfa AF: 0.579 Hom.: 3285

Bravo AF: 0.638

Asia WGS AF: 0.643 AC: 2238 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.75
DANN	Benign	0.42
PhyloP100		-0.72

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: rs2402446;

hg19: chr14-94866137;