14-35408515-T-C

Variant names:

• chr14-35408515-T-C
• rs3138045
• ENST00000848537.1:n.241+5128T>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+5128T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.213 in 152,214 control chromosomes in the GnomAD database, including 3,531 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 0.21 (3531 hom., cov: 33)
• Consequence: ENSG00000310246 ENST00000848537.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.50
• Publications: 20 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=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.234 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+5128T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.213 AC: 32328 AN: 152096 Hom.: 3528 Cov.: 33

Gnomad AFR AF: 0.237

Gnomad AMI AF: 0.191

Gnomad AMR AF: 0.192

Gnomad ASJ AF: 0.188

Gnomad EAS AF: 0.123

Gnomad SAS AF: 0.181

Gnomad FIN AF: 0.218

Gnomad MID AF: 0.209

Gnomad NFE AF: 0.212

Gnomad OTH AF: 0.195

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

GnomAD4 genome AF: 0.213 AC: 32354 AN: 152214 Hom.: 3531 Cov.: 33 AF XY: 0.209 AC XY: 15570 AN XY: 74422

African (AFR) AF: 0.237 AC: 9864 AN: 41534

American (AMR) AF: 0.193 AC: 2945 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.188 AC: 653 AN: 3470

East Asian (EAS) AF: 0.123 AC: 637 AN: 5184

South Asian (SAS) AF: 0.181 AC: 873 AN: 4826

European-Finnish (FIN) AF: 0.218 AC: 2308 AN: 10588

Middle Eastern (MID) AF: 0.204 AC: 60 AN: 294

European-Non Finnish (NFE) AF: 0.212 AC: 14433 AN: 68002

Other (OTH) AF: 0.193 AC: 408 AN: 2116

Alfa AF: 0.209 Hom.: 14823

Bravo AF: 0.213

Asia WGS AF: 0.156 AC: 547 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.11
DANN	Benign	0.51
PhyloP100		-2.5

Splicing

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

Other links and lift over

dbSNP: rs3138045; hg19: chr14-35877721;