16-51296620-G-A

Variant names:

• chr16-51296620-G-A
• rs4131099
• ENST00000642450.1:n.351-14950G>A

Variant summary

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

The ENST00000642450.1(ENSG00000285367):​n.351-14950G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.383 in 152,030 control chromosomes in the GnomAD database, including 11,781 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 0.38 (11781 hom., cov: 32)
• Consequence: ENSG00000285367 ENST00000642450.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.336
• Publications: 7 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 (EAS) allele frequency at 95% confidence interval = 0.7 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
ENSG00000285367	ENST00000642450.1	n.351-14950G>A		intron_variant	Intron 2 of 3
ENSG00000285367	ENST00000643626.1	n.52-14950G>A		intron_variant	Intron 1 of 6
ENSG00000285367	ENST00000644192.1	n.237+49529G>A		intron_variant	Intron 1 of 5

Frequencies

GnomAD3 genomes AF: 0.382 AC: 58101 AN: 151912 Hom.: 11768 Cov.: 32

Gnomad AFR AF: 0.384

Gnomad AMI AF: 0.220

Gnomad AMR AF: 0.423

Gnomad ASJ AF: 0.257

Gnomad EAS AF: 0.719

Gnomad SAS AF: 0.571

Gnomad FIN AF: 0.488

Gnomad MID AF: 0.278

Gnomad NFE AF: 0.327

Gnomad OTH AF: 0.347

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

GnomAD4 genome AF: 0.383 AC: 58156 AN: 152030 Hom.: 11781 Cov.: 32 AF XY: 0.395 AC XY: 29337 AN XY: 74294

African (AFR) AF: 0.384 AC: 15932 AN: 41484

American (AMR) AF: 0.424 AC: 6463 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.257 AC: 892 AN: 3466

East Asian (EAS) AF: 0.719 AC: 3717 AN: 5170

South Asian (SAS) AF: 0.571 AC: 2739 AN: 4800

European-Finnish (FIN) AF: 0.488 AC: 5163 AN: 10572

Middle Eastern (MID) AF: 0.282 AC: 83 AN: 294

European-Non Finnish (NFE) AF: 0.327 AC: 22224 AN: 67962

Other (OTH) AF: 0.352 AC: 742 AN: 2110

Alfa AF: 0.340 Hom.: 41325

Bravo AF: 0.375

Asia WGS AF: 0.646 AC: 2245 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.4
DANN	Benign	0.74
PhyloP100		-0.34

Splicing

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

Other links and lift over

dbSNP: rs4131099; hg19: chr16-51330531;