chr14-35417749-C-T

Variant names:

• chr14-35417749-C-T
• rs2415290
• ENST00000848537.1:n.241+14362C>T

Variant summary

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

The ENST00000848537.1(ENSG00000310246):​n.241+14362C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.813 in 152,184 control chromosomes in the GnomAD database, including 50,730 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 0.81 (50730 hom., cov: 31)
• Consequence: ENSG00000310246 ENST00000848537.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.734
• Publications: 5 publications found

Genes affected

ENSG00000310246 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.914 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
ENSG00000310246	ENST00000848537.1	n.241+14362C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.813 AC: 123600 AN: 152068 Hom.: 50663 Cov.: 31

Gnomad AFR AF: 0.922

Gnomad AMI AF: 0.639

Gnomad AMR AF: 0.822

Gnomad ASJ AF: 0.748

Gnomad EAS AF: 0.631

Gnomad SAS AF: 0.783

Gnomad FIN AF: 0.819

Gnomad MID AF: 0.747

Gnomad NFE AF: 0.767

Gnomad OTH AF: 0.765

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

GnomAD4 genome AF: 0.813 AC: 123723 AN: 152184 Hom.: 50730 Cov.: 31 AF XY: 0.813 AC XY: 60479 AN XY: 74406

African (AFR) AF: 0.922 AC: 38304 AN: 41538

American (AMR) AF: 0.823 AC: 12578 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.748 AC: 2596 AN: 3472

East Asian (EAS) AF: 0.632 AC: 3266 AN: 5170

South Asian (SAS) AF: 0.783 AC: 3775 AN: 4820

European-Finnish (FIN) AF: 0.819 AC: 8672 AN: 10592

Middle Eastern (MID) AF: 0.745 AC: 219 AN: 294

European-Non Finnish (NFE) AF: 0.767 AC: 52116 AN: 67986

Other (OTH) AF: 0.766 AC: 1617 AN: 2112

Alfa AF: 0.780 Hom.: 28516

Bravo AF: 0.818

Asia WGS AF: 0.713 AC: 2484 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.84
DANN	Benign	0.26
PhyloP100		-0.73

Splicing

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

Other links and lift over

dbSNP: rs2415290; hg19: chr14-35886955; COSMIC: COSV60063936;