chr16-55332264-C-G

Variant names:

• chr16-55332264-C-G
• rs31093
• ENST00000558730.2:n.88+1237G>C

Variant summary

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

The ENST00000558730.2(ENSG00000259283):​n.88+1237G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.339 in 151,998 control chromosomes in the GnomAD database, including 8,785 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 0.34 (8771 hom., cov: 31)
  • Exomes 𝑓: 0.39 (14 hom.)
• Consequence: ENSG00000259283 ENST00000558730.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.711
• Publications: 1 publications found

Genes affected

ENSG00000259283 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.424 is higher than 0.05.

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
ENSG00000259283	ENST00000558730.2	n.88+1237G>C		intron_variant	Intron 1 of 3	3
ENSG00000296825	ENST00000742761.1	n.118+1367C>G		intron_variant	Intron 1 of 3
ENSG00000296825	ENST00000742762.1	n.180+1217C>G		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.339 AC: 51477 AN: 151748 Hom.: 8774 Cov.: 31

Gnomad AFR AF: 0.318

Gnomad AMI AF: 0.351

Gnomad AMR AF: 0.309

Gnomad ASJ AF: 0.310

Gnomad EAS AF: 0.440

Gnomad SAS AF: 0.379

Gnomad FIN AF: 0.372

Gnomad MID AF: 0.282

Gnomad NFE AF: 0.345

Gnomad OTH AF: 0.335

GnomAD4 exome AF: 0.388 AC: 52 AN: 134 Hom.: 14 AF XY: 0.385 AC XY: 40 AN XY: 104

African (AFR) AF: 0.250 AC: 1 AN: 4

American (AMR) AF: 0.500 AC: 1 AN: 2

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.750 AC: 3 AN: 4

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 2

European-Non Finnish (NFE) AF: 0.381 AC: 45 AN: 118

Other (OTH) AF: 0.500 AC: 2 AN: 4

GnomAD4 genome AF: 0.339 AC: 51503 AN: 151864 Hom.: 8771 Cov.: 31 AF XY: 0.338 AC XY: 25085 AN XY: 74202

African (AFR) AF: 0.318 AC: 13149 AN: 41404

American (AMR) AF: 0.309 AC: 4716 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.310 AC: 1076 AN: 3468

East Asian (EAS) AF: 0.440 AC: 2246 AN: 5110

South Asian (SAS) AF: 0.378 AC: 1813 AN: 4796

European-Finnish (FIN) AF: 0.372 AC: 3934 AN: 10562

Middle Eastern (MID) AF: 0.269 AC: 79 AN: 294

European-Non Finnish (NFE) AF: 0.345 AC: 23456 AN: 67928

Other (OTH) AF: 0.339 AC: 715 AN: 2110

Alfa AF: 0.191 Hom.: 388

Bravo AF: 0.335

Asia WGS AF: 0.389 AC: 1355 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.89
DANN	Benign	0.45
PhyloP100		-0.71

Splicing

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

Other links and lift over

dbSNP: rs31093; hg19: chr16-55366176;