16-58944346-G-T

Variant names:

• chr16-58944346-G-T
• rs1865968
• ENST00000500117.1:n.680-119836G>T

Variant summary

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

The ENST00000500117.1(ENSG00000245768):​n.680-119836G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.856 in 152,194 control chromosomes in the GnomAD database, including 56,033 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 0.86 (56033 hom., cov: 32)
• Consequence: ENSG00000245768 ENST00000500117.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.995
• Publications: 3 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=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.908 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	ENST00000500117.1	n.680-119836G>T		intron_variant	Intron 2 of 3	2
ENSG00000245768	ENST00000657379.1	n.651-119836G>T		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.856 AC: 130237 AN: 152076 Hom.: 55979 Cov.: 32

Gnomad AFR AF: 0.901

Gnomad AMI AF: 0.902

Gnomad AMR AF: 0.854

Gnomad ASJ AF: 0.767

Gnomad EAS AF: 0.930

Gnomad SAS AF: 0.894

Gnomad FIN AF: 0.933

Gnomad MID AF: 0.755

Gnomad NFE AF: 0.815

Gnomad OTH AF: 0.810

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

GnomAD4 genome AF: 0.856 AC: 130352 AN: 152194 Hom.: 56033 Cov.: 32 AF XY: 0.864 AC XY: 64275 AN XY: 74412

African (AFR) AF: 0.901 AC: 37424 AN: 41538

American (AMR) AF: 0.855 AC: 13047 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.767 AC: 2660 AN: 3468

East Asian (EAS) AF: 0.930 AC: 4803 AN: 5164

South Asian (SAS) AF: 0.894 AC: 4315 AN: 4826

European-Finnish (FIN) AF: 0.933 AC: 9911 AN: 10618

Middle Eastern (MID) AF: 0.764 AC: 223 AN: 292

European-Non Finnish (NFE) AF: 0.815 AC: 55432 AN: 68002

Other (OTH) AF: 0.812 AC: 1714 AN: 2110

Alfa AF: 0.822 Hom.: 26477

Bravo AF: 0.854

Asia WGS AF: 0.910 AC: 3163 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.1
DANN	Benign	0.71
PhyloP100		-0.99

Splicing

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

Other links and lift over

dbSNP: rs1865968; hg19: chr16-58978250;