rs152303

Variant names:

• chr16-11214242-A-C
• rs152303
• ENST00000572466.2:n.187-9859A>C

Your query was ambiguous. Multiple possible variants found:

• chr16-11214242-A-C
• chr16-11214242-A-T

Variant summary

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

The ENST00000572466.2(ENSG00000263033):​n.187-9859A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.319 in 148,812 control chromosomes in the GnomAD database, including 8,048 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 0.32 (8048 hom., cov: 26)
• Consequence: ENSG00000263033 ENST00000572466.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.26
• Publications: 4 publications found

Genes affected

ENSG00000263033 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.416 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000572466.2. 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
	ENSG00000263033	ENST00000572466.2	TSL:3	n.187-9859A>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.319 AC: 47481 AN: 148712 Hom.: 8036 Cov.: 26

Gnomad AFR AF: 0.287

Gnomad AMI AF: 0.386

Gnomad AMR AF: 0.424

Gnomad ASJ AF: 0.394

Gnomad EAS AF: 0.340

Gnomad SAS AF: 0.429

Gnomad FIN AF: 0.219

Gnomad MID AF: 0.330

Gnomad NFE AF: 0.316

Gnomad OTH AF: 0.325

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

GnomAD4 genome AF: 0.319 AC: 47504 AN: 148812 Hom.: 8048 Cov.: 26 AF XY: 0.316 AC XY: 22876 AN XY: 72314

African (AFR) AF: 0.287 AC: 11574 AN: 40364

American (AMR) AF: 0.425 AC: 6220 AN: 14650

Ashkenazi Jewish (ASJ) AF: 0.394 AC: 1364 AN: 3464

East Asian (EAS) AF: 0.340 AC: 1704 AN: 5018

South Asian (SAS) AF: 0.427 AC: 2018 AN: 4726

European-Finnish (FIN) AF: 0.219 AC: 2125 AN: 9714

Middle Eastern (MID) AF: 0.325 AC: 93 AN: 286

European-Non Finnish (NFE) AF: 0.316 AC: 21393 AN: 67618

Other (OTH) AF: 0.321 AC: 663 AN: 2066

Alfa AF: 0.282 Hom.: 2107

Bravo AF: 0.338

Asia WGS AF: 0.394 AC: 1371 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	4.8
DANN	Benign	0.59
PhyloP100		1.3

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: rs152303;

hg19: chr16-11308099;