14-35415835-A-G

Variant names:

• chr14-35415835-A-G
• rs17103286
• ENST00000848537.1:n.241+12448A>G

Variant summary

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

The ENST00000848537.1(ENSG00000310246):​n.241+12448A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.505 in 152,130 control chromosomes in the GnomAD database, including 19,733 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 0.50 (19733 hom., cov: 32)
• Consequence: ENSG00000310246 ENST00000848537.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.15
• Publications: 2 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=-0.86).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.572 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+12448A>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.505 AC: 76702 AN: 152012 Hom.: 19702 Cov.: 32

Gnomad AFR AF: 0.409

Gnomad AMI AF: 0.404

Gnomad AMR AF: 0.571

Gnomad ASJ AF: 0.521

Gnomad EAS AF: 0.440

Gnomad SAS AF: 0.590

Gnomad FIN AF: 0.598

Gnomad MID AF: 0.468

Gnomad NFE AF: 0.533

Gnomad OTH AF: 0.494

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

GnomAD4 genome AF: 0.505 AC: 76778 AN: 152130 Hom.: 19733 Cov.: 32 AF XY: 0.510 AC XY: 37949 AN XY: 74382

African (AFR) AF: 0.410 AC: 16993 AN: 41496

American (AMR) AF: 0.572 AC: 8737 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.521 AC: 1808 AN: 3470

East Asian (EAS) AF: 0.442 AC: 2283 AN: 5168

South Asian (SAS) AF: 0.590 AC: 2846 AN: 4824

European-Finnish (FIN) AF: 0.598 AC: 6331 AN: 10592

Middle Eastern (MID) AF: 0.469 AC: 137 AN: 292

European-Non Finnish (NFE) AF: 0.533 AC: 36223 AN: 67982

Other (OTH) AF: 0.497 AC: 1052 AN: 2116

Alfa AF: 0.501 Hom.: 7142

Bravo AF: 0.496

Asia WGS AF: 0.517 AC: 1799 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	2.5
DANN	Benign	0.79
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs17103286; hg19: chr14-35885041;