rs205356

Variant names:

• chr16-28097207-G-A
• rs205356
• ENST00000848143.1:n.-224G>A

Variant summary

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

The ENST00000848143.1(ENSG00000310204):​n.-224G>A variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.284 in 152,064 control chromosomes in the GnomAD database, including 6,265 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 0.28 (6265 hom., cov: 32)
• Consequence: ENSG00000310204 ENST00000848143.1 upstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.713
• Publications: 6 publications found

Genes affected

ENSG00000310204 (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 (AFR) allele frequency at 95% confidence interval = 0.31 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000848143.1. 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
	ENSG00000310204	ENST00000848143.1		n.-224G>A		upstream_gene	N/A

Frequencies

GnomAD3 genomes AF: 0.284 AC: 43149 AN: 151946 Hom.: 6264 Cov.: 32

Gnomad AFR AF: 0.315

Gnomad AMI AF: 0.400

Gnomad AMR AF: 0.231

Gnomad ASJ AF: 0.330

Gnomad EAS AF: 0.104

Gnomad SAS AF: 0.131

Gnomad FIN AF: 0.292

Gnomad MID AF: 0.316

Gnomad NFE AF: 0.296

Gnomad OTH AF: 0.285

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

GnomAD4 genome AF: 0.284 AC: 43161 AN: 152064 Hom.: 6265 Cov.: 32 AF XY: 0.278 AC XY: 20689 AN XY: 74328

African (AFR) AF: 0.315 AC: 13048 AN: 41476

American (AMR) AF: 0.231 AC: 3524 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.330 AC: 1144 AN: 3470

East Asian (EAS) AF: 0.104 AC: 538 AN: 5164

South Asian (SAS) AF: 0.131 AC: 632 AN: 4820

European-Finnish (FIN) AF: 0.292 AC: 3090 AN: 10568

Middle Eastern (MID) AF: 0.330 AC: 97 AN: 294

European-Non Finnish (NFE) AF: 0.296 AC: 20123 AN: 67970

Other (OTH) AF: 0.285 AC: 601 AN: 2108

Alfa AF: 0.291 Hom.: 25581

Bravo AF: 0.285

Asia WGS AF: 0.144 AC: 502 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	0.61
DANN	Benign	0.48
PhyloP100		-0.71

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: rs205356;

hg19: chr16-28108528;

COSMIC: COSV58972607;