rs2203512

Variant names:

• chr16-27045134-G-A
• rs2203512
• ENST00000728872.1:n.93-1024C>T

Your query was ambiguous. Multiple possible variants found:

• chr16-27045134-G-A
• chr16-27045134-G-T

Variant summary

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

The ENST00000728872.1(ENSG00000295256):​n.93-1024C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.851 in 152,188 control chromosomes in the GnomAD database, including 55,472 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 0.85 (55472 hom., cov: 32)
• Consequence: ENSG00000295256 ENST00000728872.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.85
• Publications: 6 publications found

Genes affected

ENSG00000295256 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.904 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000728872.1. 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
	ENSG00000295256	ENST00000728872.1		n.93-1024C>T		intron	N/A
	ENSG00000295256	ENST00000728873.1		n.115-620C>T		intron	N/A
	ENSG00000295256	ENST00000728874.1		n.184+400C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.851 AC: 129402 AN: 152070 Hom.: 55438 Cov.: 32

Gnomad AFR AF: 0.775

Gnomad AMI AF: 0.906

Gnomad AMR AF: 0.788

Gnomad ASJ AF: 0.881

Gnomad EAS AF: 0.685

Gnomad SAS AF: 0.822

Gnomad FIN AF: 0.938

Gnomad MID AF: 0.908

Gnomad NFE AF: 0.910

Gnomad OTH AF: 0.857

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

GnomAD4 genome AF: 0.851 AC: 129489 AN: 152188 Hom.: 55472 Cov.: 32 AF XY: 0.850 AC XY: 63253 AN XY: 74396

African (AFR) AF: 0.775 AC: 32163 AN: 41490

American (AMR) AF: 0.787 AC: 12035 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.881 AC: 3057 AN: 3470

East Asian (EAS) AF: 0.686 AC: 3547 AN: 5174

South Asian (SAS) AF: 0.822 AC: 3965 AN: 4822

European-Finnish (FIN) AF: 0.938 AC: 9954 AN: 10614

Middle Eastern (MID) AF: 0.898 AC: 264 AN: 294

European-Non Finnish (NFE) AF: 0.910 AC: 61875 AN: 68028

Other (OTH) AF: 0.858 AC: 1806 AN: 2104

Alfa AF: 0.882 Hom.: 200507

Bravo AF: 0.834

Asia WGS AF: 0.787 AC: 2736 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.40
DANN	Benign	0.20
PhyloP100		-1.8

Splicing

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

Other links and lift over

dbSNP: rs2203512; hg19: chr16-27056455;