14-35415609-C-T

Variant names:

• chr14-35415609-C-T
• rs17103282
• ENST00000848537.1:n.241+12222C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The ENST00000848537.1(ENSG00000310246):​n.241+12222C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0345 in 152,328 control chromosomes in the GnomAD database, including 114 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 0.035 (114 hom., cov: 33)
• Consequence: ENSG00000310246 ENST00000848537.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.138
• 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=-0.86).
• BS1: Variant frequency is greater than expected in population amr. GnomAd4 allele frequency = 0.0345 (5258/152328) while in subpopulation AMR AF = 0.0425 (651/15300). AF 95% confidence interval is 0.0398. There are 114 homozygotes in GnomAd4. There are 2423 alleles in the male GnomAd4 subpopulation. Median coverage is 33. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 114 gene

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+12222C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.0345 AC: 5246 AN: 152210 Hom.: 112 Cov.: 33

Gnomad AFR AF: 0.0292

Gnomad AMI AF: 0.0110

Gnomad AMR AF: 0.0426

Gnomad ASJ AF: 0.0861

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.0118

Gnomad FIN AF: 0.0164

Gnomad MID AF: 0.0665

Gnomad NFE AF: 0.0404

Gnomad OTH AF: 0.0340

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

GnomAD4 genome AF: 0.0345 AC: 5258 AN: 152328 Hom.: 114 Cov.: 33 AF XY: 0.0325 AC XY: 2423 AN XY: 74480

African (AFR) AF: 0.0295 AC: 1225 AN: 41570

American (AMR) AF: 0.0425 AC: 651 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.0861 AC: 299 AN: 3472

East Asian (EAS) AF: 0.00 AC: 0 AN: 5188

South Asian (SAS) AF: 0.0114 AC: 55 AN: 4832

European-Finnish (FIN) AF: 0.0164 AC: 174 AN: 10622

Middle Eastern (MID) AF: 0.0714 AC: 21 AN: 294

European-Non Finnish (NFE) AF: 0.0405 AC: 2752 AN: 68028

Other (OTH) AF: 0.0336 AC: 71 AN: 2110

Alfa AF: 0.0372 Hom.: 85

Bravo AF: 0.0361

Asia WGS AF: 0.0110 AC: 38 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	5.9
DANN	Benign	0.62
PhyloP100		-0.14

Splicing

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

Other links and lift over

dbSNP: rs17103282; hg19: chr14-35884815;