16-59114038-C-T

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 4 publications found

Genes affected

ENSG00000245768 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.0984 AC: 4082 AN: 41498

American (AMR) AF: 0.376 AC: 5744 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.343 AC: 1191 AN: 3472

East Asian (EAS) AF: 0.410 AC: 2112 AN: 5152

South Asian (SAS) AF: 0.555 AC: 2675 AN: 4822

European-Finnish (FIN) AF: 0.486 AC: 5133 AN: 10556

Middle Eastern (MID) AF: 0.371 AC: 109 AN: 294

European-Non Finnish (NFE) AF: 0.488 AC: 33173 AN: 67910

Other (OTH) AF: 0.376 AC: 791 AN: 2106

Alfa AF: 0.434 Hom.: 7747

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
PhyloP100		-0.27

Splicing

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

Other links and lift over

dbSNP: rs4238802; hg19: chr16-59147942;