ENST00000416510.1:n.168-28687T>A

Variant names:

• chr1-222247176-A-T
• rs158724
• ENST00000416510.1:n.168-28687T>A

Variant summary

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

The ENST00000416510.1(ENSG00000236230):​n.168-28687T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.698 in 152,112 control chromosomes in the GnomAD database, including 37,748 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 0.70 (37748 hom., cov: 32)
• Consequence: ENSG00000236230 ENST00000416510.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.822
• Publications: 3 publications found

Genes affected

ENSG00000236230 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.839 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000416510.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000236230	ENST00000416510.1	TSL:1	n.168-28687T>A		intron	N/A
	ENSG00000236230	ENST00000652067.1		n.420-58450T>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.698 AC: 106054 AN: 151994 Hom.: 37698 Cov.: 32

Gnomad AFR AF: 0.846

Gnomad AMI AF: 0.779

Gnomad AMR AF: 0.599

Gnomad ASJ AF: 0.629

Gnomad EAS AF: 0.533

Gnomad SAS AF: 0.759

Gnomad FIN AF: 0.631

Gnomad MID AF: 0.766

Gnomad NFE AF: 0.651

Gnomad OTH AF: 0.685

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

GnomAD4 genome AF: 0.698 AC: 106161 AN: 152112 Hom.: 37748 Cov.: 32 AF XY: 0.693 AC XY: 51542 AN XY: 74376

African (AFR) AF: 0.846 AC: 35123 AN: 41510

American (AMR) AF: 0.600 AC: 9165 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.629 AC: 2184 AN: 3472

East Asian (EAS) AF: 0.532 AC: 2740 AN: 5152

South Asian (SAS) AF: 0.758 AC: 3660 AN: 4826

European-Finnish (FIN) AF: 0.631 AC: 6682 AN: 10582

Middle Eastern (MID) AF: 0.776 AC: 228 AN: 294

European-Non Finnish (NFE) AF: 0.651 AC: 44223 AN: 67970

Other (OTH) AF: 0.686 AC: 1449 AN: 2112

Alfa AF: 0.556 Hom.: 1467

Bravo AF: 0.705

Asia WGS AF: 0.724 AC: 2519 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.82
DANN	Benign	0.58
PhyloP100		-0.82

Splicing

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

Other links and lift over

dbSNP: rs158724; hg19: chr1-222420518;