chr16-52548864-A-T

Variant names:

• chr16-52548864-A-T
• rs45492607
• ENST00000826650.1:n.102+2352A>T

Variant summary

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

The ENST00000826650.1(ENSG00000285800):​n.102+2352A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. 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 0.023 (12 hom., cov: 0)
• Consequence: ENSG00000285800 ENST00000826650.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.55
• Publications: 0 publications found

Genes affected

ENSG00000285800 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BS1: Variant frequency is greater than expected in population afr. GnomAd4 allele frequency = 0.0226 (1473/65272) while in subpopulation AFR AF = 0.0503 (564/11220). AF 95% confidence interval is 0.0468. There are 12 homozygotes in GnomAd4. There are 705 alleles in the male GnomAd4 subpopulation. Median coverage is 0. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 12 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
ENSG00000285800	ENST00000826650.1	n.102+2352A>T		intron_variant	Intron 1 of 2
ENSG00000285800	ENST00000826651.1	n.89+2352A>T		intron_variant	Intron 1 of 5
ENSG00000285800	ENST00000826652.1	n.104+2304A>T		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.0226 AC: 1474 AN: 65280 Hom.: 12 Cov.: 0

Gnomad AFR AF: 0.0503

Gnomad AMI AF: 0.0516

Gnomad AMR AF: 0.0157

Gnomad ASJ AF: 0.0266

Gnomad EAS AF: 0.0130

Gnomad SAS AF: 0.0352

Gnomad FIN AF: 0.00408

Gnomad MID AF: 0.0846

Gnomad NFE AF: 0.0164

Gnomad OTH AF: 0.0202

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

GnomAD4 genome AF: 0.0226 AC: 1473 AN: 65272 Hom.: 12 Cov.: 0 AF XY: 0.0223 AC XY: 705 AN XY: 31554

African (AFR) AF: 0.0503 AC: 564 AN: 11220

American (AMR) AF: 0.0157 AC: 94 AN: 5998

Ashkenazi Jewish (ASJ) AF: 0.0266 AC: 36 AN: 1354

East Asian (EAS) AF: 0.0130 AC: 10 AN: 770

South Asian (SAS) AF: 0.0348 AC: 93 AN: 2670

European-Finnish (FIN) AF: 0.00408 AC: 20 AN: 4904

Middle Eastern (MID) AF: 0.0917 AC: 11 AN: 120

European-Non Finnish (NFE) AF: 0.0164 AC: 604 AN: 36898

Other (OTH) AF: 0.0202 AC: 18 AN: 892

Alfa AF: 0.0115 Hom.: 1

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.031
DANN	Benign	0.35
PhyloP100		-1.6

Splicing

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

Other links and lift over

dbSNP: rs45492607; hg19: chr16-52582776;