8-16856482-C-T

Variant names:

• chr8-16856482-C-T
• rs477516
• ENST00000521411.2:n.128-12227G>A

Variant summary

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

The ENST00000755781.1(ENSG00000253496):​n.228+58436G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.311 in 152,018 control chromosomes in the GnomAD database, including 7,696 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 0.31 (7696 hom., cov: 32)
• Consequence: ENSG00000253496 ENST00000755781.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.160
• Publications: 6 publications found

Genes affected

ENSG00000253496 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.514 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000755781.1. 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
	ENSG00000253496	ENST00000521411.2	TSL:5	n.128-12227G>A		intron	N/A
	ENSG00000253496	ENST00000755781.1		n.228+58436G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.311 AC: 47299 AN: 151900 Hom.: 7696 Cov.: 32

Gnomad AFR AF: 0.325

Gnomad AMI AF: 0.164

Gnomad AMR AF: 0.352

Gnomad ASJ AF: 0.242

Gnomad EAS AF: 0.385

Gnomad SAS AF: 0.532

Gnomad FIN AF: 0.338

Gnomad MID AF: 0.263

Gnomad NFE AF: 0.275

Gnomad OTH AF: 0.280

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

GnomAD4 genome AF: 0.311 AC: 47331 AN: 152018 Hom.: 7696 Cov.: 32 AF XY: 0.323 AC XY: 24001 AN XY: 74300

African (AFR) AF: 0.325 AC: 13464 AN: 41450

American (AMR) AF: 0.351 AC: 5365 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.242 AC: 841 AN: 3472

East Asian (EAS) AF: 0.384 AC: 1987 AN: 5168

South Asian (SAS) AF: 0.532 AC: 2562 AN: 4820

European-Finnish (FIN) AF: 0.338 AC: 3569 AN: 10554

Middle Eastern (MID) AF: 0.252 AC: 74 AN: 294

European-Non Finnish (NFE) AF: 0.275 AC: 18719 AN: 67964

Other (OTH) AF: 0.285 AC: 601 AN: 2112

Alfa AF: 0.286 Hom.: 27744

Bravo AF: 0.310

Asia WGS AF: 0.431 AC: 1500 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	5.6
DANN	Benign	0.44
PhyloP100		0.16

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs477516;

hg19: chr8-16713991;