14-35416080-T-C

Variant names:

• chr14-35416080-T-C
• rs8018407
• ENST00000848537.1:n.241+12693T>C

Variant summary

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

The ENST00000848537.1(ENSG00000310246):​n.241+12693T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.696 in 152,126 control chromosomes in the GnomAD database, including 36,897 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 0.70 (36897 hom., cov: 33)
• Consequence: ENSG00000310246 ENST00000848537.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.58
• Publications: 4 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=-0.73).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.724 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000848537.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000310246	ENST00000848537.1		n.241+12693T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.696 AC: 105797 AN: 152008 Hom.: 36836 Cov.: 33

Gnomad AFR AF: 0.731

Gnomad AMI AF: 0.501

Gnomad AMR AF: 0.730

Gnomad ASJ AF: 0.702

Gnomad EAS AF: 0.728

Gnomad SAS AF: 0.728

Gnomad FIN AF: 0.726

Gnomad MID AF: 0.677

Gnomad NFE AF: 0.661

Gnomad OTH AF: 0.689

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

GnomAD4 genome AF: 0.696 AC: 105916 AN: 152126 Hom.: 36897 Cov.: 33 AF XY: 0.699 AC XY: 51961 AN XY: 74362

African (AFR) AF: 0.731 AC: 30318 AN: 41478

American (AMR) AF: 0.730 AC: 11167 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.702 AC: 2437 AN: 3472

East Asian (EAS) AF: 0.728 AC: 3772 AN: 5178

South Asian (SAS) AF: 0.728 AC: 3512 AN: 4822

European-Finnish (FIN) AF: 0.726 AC: 7670 AN: 10572

Middle Eastern (MID) AF: 0.680 AC: 200 AN: 294

European-Non Finnish (NFE) AF: 0.661 AC: 44924 AN: 67994

Other (OTH) AF: 0.691 AC: 1459 AN: 2110

Alfa AF: 0.686 Hom.: 12513

Bravo AF: 0.698

Asia WGS AF: 0.752 AC: 2613 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.73
CADD	Benign	13
DANN	Benign	0.85
PhyloP100		1.6

Splicing

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

Other links and lift over

dbSNP: rs8018407; hg19: chr14-35885286;