ENST00000500117.1:n.749+21450A>G

Variant names:

• chr16-59085701-A-G
• rs10221112
• ENST00000500117.1:n.749+21450A>G

Variant summary

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

The ENST00000500117.1(ENSG00000245768):​n.749+21450A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.322 in 151,614 control chromosomes in the GnomAD database, including 8,062 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 0.32 (8062 hom., cov: 31)
• Consequence: ENSG00000245768 ENST00000500117.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.448
• Publications: 2 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=-1.02).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.335 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.749+21450A>G		intron_variant	Intron 3 of 3	2
ENSG00000245768	ENST00000657379.1	n.720+21450A>G		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.322 AC: 48780 AN: 151496 Hom.: 8054 Cov.: 31

Gnomad AFR AF: 0.310

Gnomad AMI AF: 0.402

Gnomad AMR AF: 0.275

Gnomad ASJ AF: 0.375

Gnomad EAS AF: 0.127

Gnomad SAS AF: 0.304

Gnomad FIN AF: 0.412

Gnomad MID AF: 0.418

Gnomad NFE AF: 0.338

Gnomad OTH AF: 0.315

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

GnomAD4 genome AF: 0.322 AC: 48823 AN: 151614 Hom.: 8062 Cov.: 31 AF XY: 0.322 AC XY: 23807 AN XY: 74042

African (AFR) AF: 0.311 AC: 12824 AN: 41298

American (AMR) AF: 0.274 AC: 4170 AN: 15192

Ashkenazi Jewish (ASJ) AF: 0.375 AC: 1299 AN: 3466

East Asian (EAS) AF: 0.126 AC: 654 AN: 5180

South Asian (SAS) AF: 0.304 AC: 1463 AN: 4818

European-Finnish (FIN) AF: 0.412 AC: 4302 AN: 10450

Middle Eastern (MID) AF: 0.422 AC: 124 AN: 294

European-Non Finnish (NFE) AF: 0.338 AC: 22968 AN: 67906

Other (OTH) AF: 0.311 AC: 655 AN: 2104

Alfa AF: 0.330 Hom.: 4210

Bravo AF: 0.312

Asia WGS AF: 0.224 AC: 778 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.3
DANN	Benign	0.48
PhyloP100		-0.45

Splicing

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

Other links and lift over

dbSNP: rs10221112; hg19: chr16-59119605;