chr8-16620602-C-G

Variant names:

• chr8-16620602-C-G
• rs822300
• ENST00000521055.1:n.288+16060C>G

Variant summary

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

The ENST00000521055.1(ENSG00000253184):​n.288+16060C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.408 in 151,612 control chromosomes in the GnomAD database, including 13,125 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 0.41 (13125 hom., cov: 32)
• Consequence: ENSG00000253184 ENST00000521055.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0430
• Publications: 2 publications found

Genes affected

ENSG00000253184 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.443 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000521055.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000253184	ENST00000521055.1	TSL:3	n.288+16060C>G		intron	N/A
	ENSG00000253496	ENST00000649038.1		n.1075-21682G>C		intron	N/A
	ENSG00000253496	ENST00000755792.1		n.500-119G>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.408 AC: 61735 AN: 151494 Hom.: 13109 Cov.: 32

Gnomad AFR AF: 0.404

Gnomad AMI AF: 0.279

Gnomad AMR AF: 0.338

Gnomad ASJ AF: 0.408

Gnomad EAS AF: 0.0513

Gnomad SAS AF: 0.306

Gnomad FIN AF: 0.503

Gnomad MID AF: 0.433

Gnomad NFE AF: 0.447

Gnomad OTH AF: 0.383

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

GnomAD4 genome AF: 0.408 AC: 61792 AN: 151612 Hom.: 13125 Cov.: 32 AF XY: 0.404 AC XY: 29970 AN XY: 74094

African (AFR) AF: 0.404 AC: 16716 AN: 41408

American (AMR) AF: 0.337 AC: 5133 AN: 15216

Ashkenazi Jewish (ASJ) AF: 0.408 AC: 1410 AN: 3456

East Asian (EAS) AF: 0.0519 AC: 265 AN: 5110

South Asian (SAS) AF: 0.307 AC: 1480 AN: 4820

European-Finnish (FIN) AF: 0.503 AC: 5317 AN: 10574

Middle Eastern (MID) AF: 0.449 AC: 131 AN: 292

European-Non Finnish (NFE) AF: 0.447 AC: 30286 AN: 67744

Other (OTH) AF: 0.383 AC: 806 AN: 2104

Alfa AF: 0.427 Hom.: 1769

Bravo AF: 0.392

Asia WGS AF: 0.209 AC: 732 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.1
DANN	Benign	0.59
PhyloP100		-0.043

Splicing

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

Other links and lift over

dbSNP: rs822300; hg19: chr8-16478111;