14-87274681-C-T

Variant names:

• chr14-87274681-C-T
• rs1756650
• ENST00000849835.1:n.96+17803C>T

Variant summary

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

The ENST00000849835.1(ENSG00000310449):​n.96+17803C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.84 in 152,030 control chromosomes in the GnomAD database, including 54,855 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 0.84 (54855 hom., cov: 31)
• Consequence: ENSG00000310449 ENST00000849835.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.325
• Publications: 6 publications found

Genes affected

ENSG00000310449 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.926 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000310449	ENST00000849835.1	n.96+17803C>T		intron_variant	Intron 1 of 3
ENSG00000310462	ENST00000850009.1	n.227+10846G>A		intron_variant	Intron 3 of 4
ENSG00000310462	ENST00000850010.1	n.83+14865G>A		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.840 AC: 127665 AN: 151912 Hom.: 54828 Cov.: 31

Gnomad AFR AF: 0.648

Gnomad AMI AF: 0.814

Gnomad AMR AF: 0.921

Gnomad ASJ AF: 0.936

Gnomad EAS AF: 0.834

Gnomad SAS AF: 0.949

Gnomad FIN AF: 0.941

Gnomad MID AF: 0.943

Gnomad NFE AF: 0.910

Gnomad OTH AF: 0.866

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

GnomAD4 genome AF: 0.840 AC: 127742 AN: 152030 Hom.: 54855 Cov.: 31 AF XY: 0.846 AC XY: 62874 AN XY: 74304

African (AFR) AF: 0.648 AC: 26832 AN: 41412

American (AMR) AF: 0.921 AC: 14060 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.936 AC: 3250 AN: 3472

East Asian (EAS) AF: 0.834 AC: 4292 AN: 5146

South Asian (SAS) AF: 0.949 AC: 4585 AN: 4830

European-Finnish (FIN) AF: 0.941 AC: 9973 AN: 10602

Middle Eastern (MID) AF: 0.946 AC: 278 AN: 294

European-Non Finnish (NFE) AF: 0.910 AC: 61898 AN: 67992

Other (OTH) AF: 0.867 AC: 1833 AN: 2114

Alfa AF: 0.898 Hom.: 182633

Bravo AF: 0.829

Asia WGS AF: 0.889 AC: 3094 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.0
DANN	Benign	0.70
PhyloP100		-0.33

Splicing

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

Other links and lift over

dbSNP: rs1756650; hg19: chr14-87741025;