chr16-59114038-C-T

Variant names:

• chr16-59114038-C-T
• rs4238802
• ENST00000657379.1:n.720+49787C>T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000657379.1(ENSG00000245768):​n.720+49787C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.365 in 151,992 control chromosomes in the GnomAD database, including 12,395 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 0.37 (12395 hom., cov: 32)
• Consequence: ENSG00000245768 ENST00000657379.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.269

Genes affected

ENSG00000245768 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.537 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
ENSG00000245768	ENST00000657379.1	n.720+49787C>T		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.365 AC: 55505 AN: 151876 Hom.: 12395 Cov.: 32

Gnomad AFR AF: 0.0985

Gnomad AMI AF: 0.542

Gnomad AMR AF: 0.377

Gnomad ASJ AF: 0.343

Gnomad EAS AF: 0.410

Gnomad SAS AF: 0.554

Gnomad FIN AF: 0.486

Gnomad MID AF: 0.370

Gnomad NFE AF: 0.488

Gnomad OTH AF: 0.377

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

GnomAD4 genome AF: 0.365 AC: 55503 AN: 151992 Hom.: 12395 Cov.: 32 AF XY: 0.369 AC XY: 27414 AN XY: 74296

Gnomad4 AFR AF: 0.0984

Gnomad4 AMR AF: 0.376

Gnomad4 ASJ AF: 0.343

Gnomad4 EAS AF: 0.410

Gnomad4 SAS AF: 0.555

Gnomad4 FIN AF: 0.486

Gnomad4 NFE AF: 0.488

Gnomad4 OTH AF: 0.376

Alfa AF: 0.430 Hom.: 6864

Bravo AF: 0.341

Asia WGS AF: 0.404 AC: 1404 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	3.2
DANN	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4238802; hg19: chr16-59147942;