16-51271296-C-T

Variant names:

• chr16-51271296-C-T
• rs10521229
• ENST00000642450.1:n.351-40274C>T

Variant summary

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

The ENST00000642450.1(ENSG00000285367):​n.351-40274C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0398 in 152,260 control chromosomes in the GnomAD database, including 259 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 0.040 (259 hom., cov: 33)
• Consequence: ENSG00000285367 ENST00000642450.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.95
• Publications: 2 publications found

Genes affected

ENSG00000285367 (HGNC:58539):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.5).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.226 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000642450.1. 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
	ENSG00000285367	ENST00000642450.1		n.351-40274C>T		intron	N/A
	ENSG00000285367	ENST00000643626.1		n.52-40274C>T		intron	N/A
	ENSG00000285367	ENST00000644069.1		n.334-935C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0399 AC: 6070 AN: 152142 Hom.: 260 Cov.: 33

Gnomad AFR AF: 0.0478

Gnomad AMI AF: 0.00768

Gnomad AMR AF: 0.0757

Gnomad ASJ AF: 0.0323

Gnomad EAS AF: 0.238

Gnomad SAS AF: 0.0407

Gnomad FIN AF: 0.0382

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0132

Gnomad OTH AF: 0.0368

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

GnomAD4 genome AF: 0.0398 AC: 6064 AN: 152260 Hom.: 259 Cov.: 33 AF XY: 0.0417 AC XY: 3105 AN XY: 74450

African (AFR) AF: 0.0478 AC: 1985 AN: 41552

American (AMR) AF: 0.0755 AC: 1154 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.0323 AC: 112 AN: 3470

East Asian (EAS) AF: 0.237 AC: 1228 AN: 5180

South Asian (SAS) AF: 0.0401 AC: 193 AN: 4816

European-Finnish (FIN) AF: 0.0382 AC: 405 AN: 10606

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 294

European-Non Finnish (NFE) AF: 0.0132 AC: 899 AN: 68026

Other (OTH) AF: 0.0383 AC: 81 AN: 2114

Alfa AF: 0.0227 Hom.: 29

Bravo AF: 0.0452

Asia WGS AF: 0.138 AC: 477 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.50
CADD	Benign	15
DANN	Benign	0.56
PhyloP100		1.9

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: rs10521229;

hg19: chr16-51305207;