rs2402446

Positions:

• chr14-94399800-T-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000693506.1(ENSG00000289541):​n.124+8906T>A variant causes a intron, non coding transcript 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: ENST00000693506.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.717

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000693506.1	n.124+8906T>A		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.820

Gnomad4 AMR AF: 0.572

Gnomad4 ASJ AF: 0.633

Gnomad4 EAS AF: 0.610

Gnomad4 SAS AF: 0.723

Gnomad4 FIN AF: 0.562

Gnomad4 NFE AF: 0.543

Gnomad4 OTH AF: 0.629

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 v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2402446; hg19: chr14-94866137;