chr16-51124799-C-T

Variant names:

• chr16-51124799-C-T
• rs10521222
• ENST00000752033.1:n.132-6584C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The ENST00000752033.1(ENSG00000297955):​n.132-6584C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.032 in 152,294 control chromosomes in the GnomAD database, including 121 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 0.032 (121 hom., cov: 33)
• Consequence: ENSG00000297955 ENST00000752033.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.78
• Publications: 37 publications found

Genes affected

ENSG00000297955 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BS1: Variant frequency is greater than expected in population nfe. GnomAd4 allele frequency = 0.032 (4872/152294) while in subpopulation NFE AF = 0.0478 (3252/68022). AF 95% confidence interval is 0.0464. There are 121 homozygotes in GnomAd4. There are 2257 alleles in the male GnomAd4 subpopulation. Median coverage is 33. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 121 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000297955	ENST00000752033.1	n.132-6584C>T		intron_variant	Intron 1 of 2
ENSG00000297955	ENST00000752034.1	n.63+4205C>T		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.0320 AC: 4873 AN: 152176 Hom.: 121 Cov.: 33

Gnomad AFR AF: 0.00951

Gnomad AMI AF: 0.0648

Gnomad AMR AF: 0.0284

Gnomad ASJ AF: 0.0789

Gnomad EAS AF: 0.000577

Gnomad SAS AF: 0.0170

Gnomad FIN AF: 0.0251

Gnomad MID AF: 0.0823

Gnomad NFE AF: 0.0478

Gnomad OTH AF: 0.0397

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

GnomAD4 genome AF: 0.0320 AC: 4872 AN: 152294 Hom.: 121 Cov.: 33 AF XY: 0.0303 AC XY: 2257 AN XY: 74478

African (AFR) AF: 0.00948 AC: 394 AN: 41550

American (AMR) AF: 0.0284 AC: 434 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.0789 AC: 274 AN: 3472

East Asian (EAS) AF: 0.000578 AC: 3 AN: 5190

South Asian (SAS) AF: 0.0170 AC: 82 AN: 4826

European-Finnish (FIN) AF: 0.0251 AC: 266 AN: 10614

Middle Eastern (MID) AF: 0.0850 AC: 25 AN: 294

European-Non Finnish (NFE) AF: 0.0478 AC: 3252 AN: 68022

Other (OTH) AF: 0.0393 AC: 83 AN: 2114

Alfa AF: 0.0449 Hom.: 539

Bravo AF: 0.0329

Asia WGS AF: 0.00635 AC: 23 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.050
DANN	Benign	0.50
PhyloP100		-1.8

Splicing

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

Other links and lift over

dbSNP: rs10521222; hg19: chr16-51158710;