rs16880206

Variant names:

• chr8-109985793-T-C
• rs16880206
• ENST00000820221.1:n.44+11134T>C

Variant summary

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

The ENST00000820221.1(ENSG00000255402):​n.44+11134T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0966 in 152,176 control chromosomes in the GnomAD database, including 1,877 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 0.097 (1877 hom., cov: 32)
• Consequence: ENSG00000255402 ENST00000820221.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.03
• Publications: 0 publications found

Genes affected

ENSG00000255402 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.293 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000820221.1. 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000255402	ENST00000820221.1		n.44+11134T>C		intron	N/A
	ENSG00000255402	ENST00000820222.1		n.90+11134T>C		intron	N/A
	ENSG00000255402	ENST00000820223.1		n.204+10130T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0965 AC: 14677 AN: 152056 Hom.: 1872 Cov.: 32

Gnomad AFR AF: 0.297

Gnomad AMI AF: 0.0341

Gnomad AMR AF: 0.0434

Gnomad ASJ AF: 0.0118

Gnomad EAS AF: 0.000193

Gnomad SAS AF: 0.0209

Gnomad FIN AF: 0.00264

Gnomad MID AF: 0.0222

Gnomad NFE AF: 0.0198

Gnomad OTH AF: 0.0723

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

GnomAD4 genome AF: 0.0966 AC: 14700 AN: 152176 Hom.: 1877 Cov.: 32 AF XY: 0.0929 AC XY: 6913 AN XY: 74412

African (AFR) AF: 0.297 AC: 12332 AN: 41490

American (AMR) AF: 0.0434 AC: 663 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.0118 AC: 41 AN: 3468

East Asian (EAS) AF: 0.000193 AC: 1 AN: 5178

South Asian (SAS) AF: 0.0203 AC: 98 AN: 4826

European-Finnish (FIN) AF: 0.00264 AC: 28 AN: 10622

Middle Eastern (MID) AF: 0.0238 AC: 7 AN: 294

European-Non Finnish (NFE) AF: 0.0198 AC: 1348 AN: 67992

Other (OTH) AF: 0.0716 AC: 151 AN: 2110

Alfa AF: 0.0589 Hom.: 307

Bravo AF: 0.109

Asia WGS AF: 0.0230 AC: 82 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	6.5
DANN	Benign	0.81
PhyloP100		1.0

Splicing

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

Other links and lift over

dbSNP: rs16880206; hg19: chr8-110998022;