chr16-51166620-T-G

Variant names:

• chr16-51166620-T-G
• rs4785239
• ENST00000642450.1:n.294+15557T>G

Variant summary

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

The ENST00000642450.1(ENSG00000285367):​n.294+15557T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.738 in 152,060 control chromosomes in the GnomAD database, including 42,797 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 0.74 (42797 hom., cov: 32)
• Consequence: ENSG00000285367 ENST00000642450.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.641
• Publications: 6 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=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.852 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.294+15557T>G		intron	N/A
	ENSG00000285367	ENST00000643626.1		n.51+14445T>G		intron	N/A
	ENSG00000285367	ENST00000644069.1		n.55+14445T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.738 AC: 112139 AN: 151942 Hom.: 42778 Cov.: 32

Gnomad AFR AF: 0.530

Gnomad AMI AF: 0.793

Gnomad AMR AF: 0.723

Gnomad ASJ AF: 0.786

Gnomad EAS AF: 0.637

Gnomad SAS AF: 0.874

Gnomad FIN AF: 0.871

Gnomad MID AF: 0.801

Gnomad NFE AF: 0.841

Gnomad OTH AF: 0.747

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

GnomAD4 genome AF: 0.738 AC: 112203 AN: 152060 Hom.: 42797 Cov.: 32 AF XY: 0.741 AC XY: 55074 AN XY: 74336

African (AFR) AF: 0.530 AC: 21953 AN: 41428

American (AMR) AF: 0.722 AC: 11030 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.786 AC: 2729 AN: 3472

East Asian (EAS) AF: 0.638 AC: 3297 AN: 5170

South Asian (SAS) AF: 0.874 AC: 4208 AN: 4814

European-Finnish (FIN) AF: 0.871 AC: 9223 AN: 10584

Middle Eastern (MID) AF: 0.803 AC: 236 AN: 294

European-Non Finnish (NFE) AF: 0.841 AC: 57225 AN: 68004

Other (OTH) AF: 0.748 AC: 1579 AN: 2112

Alfa AF: 0.804 Hom.: 26617

Bravo AF: 0.713

Asia WGS AF: 0.747 AC: 2599 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.54
DANN	Benign	0.41
PhyloP100		-0.64

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: rs4785239;

hg19: chr16-51200531;