chr14-38108328-A-G

Variant names:

• chr14-38108328-A-G
• rs2415438
• ENST00000554687.1:n.200+60012T>C

Variant summary

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

The ENST00000554687.1(ENSG00000259048):​n.200+60012T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.678 in 152,020 control chromosomes in the GnomAD database, including 36,159 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 0.68 (36159 hom., cov: 32)
• Consequence: ENSG00000259048 ENST00000554687.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.212
• Publications: 5 publications found

Genes affected

ENSG00000259048 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.853 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
ENSG00000259048	ENST00000554687.1	n.200+60012T>C		intron_variant	Intron 2 of 4	4

Frequencies

GnomAD3 genomes AF: 0.678 AC: 102928 AN: 151902 Hom.: 36114 Cov.: 32

Gnomad AFR AF: 0.860

Gnomad AMI AF: 0.640

Gnomad AMR AF: 0.662

Gnomad ASJ AF: 0.611

Gnomad EAS AF: 0.390

Gnomad SAS AF: 0.570

Gnomad FIN AF: 0.577

Gnomad MID AF: 0.642

Gnomad NFE AF: 0.620

Gnomad OTH AF: 0.667

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

GnomAD4 genome AF: 0.678 AC: 103029 AN: 152020 Hom.: 36159 Cov.: 32 AF XY: 0.674 AC XY: 50065 AN XY: 74314

African (AFR) AF: 0.860 AC: 35702 AN: 41508

American (AMR) AF: 0.662 AC: 10101 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.611 AC: 2116 AN: 3466

East Asian (EAS) AF: 0.390 AC: 2019 AN: 5180

South Asian (SAS) AF: 0.569 AC: 2746 AN: 4828

European-Finnish (FIN) AF: 0.577 AC: 6069 AN: 10522

Middle Eastern (MID) AF: 0.639 AC: 188 AN: 294

European-Non Finnish (NFE) AF: 0.620 AC: 42109 AN: 67952

Other (OTH) AF: 0.663 AC: 1397 AN: 2108

Alfa AF: 0.632 Hom.: 129559

Bravo AF: 0.690

Asia WGS AF: 0.511 AC: 1770 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	3.0
DANN	Benign	0.77
PhyloP100		-0.21

Splicing

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

Other links and lift over

dbSNP: rs2415438; hg19: chr14-38577533;