chr16-76128092-G-A

Variant names:

• chr16-76128092-G-A
• rs4888473
• ENST00000564561.1:n.262+12270C>T

Variant summary

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

The ENST00000564561.1(ENSG00000260223):​n.262+12270C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.22 in 152,014 control chromosomes in the GnomAD database, including 5,138 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 0.22 (5138 hom., cov: 32)
• Consequence: ENSG00000260223 ENST00000564561.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.277
• Publications: 1 publications found

Genes affected

ENSG00000260223 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.787 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000564561.1. 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
	ENSG00000260223	ENST00000564561.1	TSL:2	n.262+12270C>T		intron	N/A
	ENSG00000260223	ENST00000808909.1		n.238+19468C>T		intron	N/A
	ENSG00000260223	ENST00000808910.1		n.185+19468C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.220 AC: 33350 AN: 151896 Hom.: 5120 Cov.: 32

Gnomad AFR AF: 0.144

Gnomad AMI AF: 0.143

Gnomad AMR AF: 0.392

Gnomad ASJ AF: 0.204

Gnomad EAS AF: 0.807

Gnomad SAS AF: 0.214

Gnomad FIN AF: 0.257

Gnomad MID AF: 0.206

Gnomad NFE AF: 0.177

Gnomad OTH AF: 0.253

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

GnomAD4 genome AF: 0.220 AC: 33384 AN: 152014 Hom.: 5138 Cov.: 32 AF XY: 0.231 AC XY: 17185 AN XY: 74294

African (AFR) AF: 0.145 AC: 6001 AN: 41470

American (AMR) AF: 0.393 AC: 6005 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.204 AC: 708 AN: 3470

East Asian (EAS) AF: 0.807 AC: 4174 AN: 5170

South Asian (SAS) AF: 0.214 AC: 1031 AN: 4816

European-Finnish (FIN) AF: 0.257 AC: 2699 AN: 10516

Middle Eastern (MID) AF: 0.207 AC: 61 AN: 294

European-Non Finnish (NFE) AF: 0.177 AC: 12046 AN: 67986

Other (OTH) AF: 0.251 AC: 529 AN: 2108

Alfa AF: 0.184 Hom.: 431

Bravo AF: 0.236

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	3.3
DANN	Benign	0.23
PhyloP100		-0.28

Splicing

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

Other links and lift over

dbSNP: rs4888473; hg19: chr16-76161990;