16-66124833-A-T

Variant names:

• chr16-66124833-A-T
• rs8050896
• ENST00000787386.1:n.674+4305T>A

Variant summary

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

The ENST00000787386.1(ENSG00000302504):​n.674+4305T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.146 in 152,120 control chromosomes in the GnomAD database, including 2,560 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 0.15 (2560 hom., cov: 31)
• Consequence: ENSG00000302504 ENST00000787386.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.147
• Publications: 13 publications found

Genes affected

ENSG00000302504 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.317 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
ENSG00000302504	ENST00000787386.1	n.674+4305T>A		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.146 AC: 22149 AN: 152002 Hom.: 2560 Cov.: 31

Gnomad AFR AF: 0.322

Gnomad AMI AF: 0.117

Gnomad AMR AF: 0.114

Gnomad ASJ AF: 0.129

Gnomad EAS AF: 0.0277

Gnomad SAS AF: 0.0573

Gnomad FIN AF: 0.0718

Gnomad MID AF: 0.130

Gnomad NFE AF: 0.0742

Gnomad OTH AF: 0.138

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

GnomAD4 genome AF: 0.146 AC: 22177 AN: 152120 Hom.: 2560 Cov.: 31 AF XY: 0.144 AC XY: 10708 AN XY: 74364

African (AFR) AF: 0.321 AC: 13326 AN: 41450

American (AMR) AF: 0.114 AC: 1743 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.129 AC: 448 AN: 3472

East Asian (EAS) AF: 0.0276 AC: 143 AN: 5188

South Asian (SAS) AF: 0.0570 AC: 275 AN: 4826

European-Finnish (FIN) AF: 0.0718 AC: 760 AN: 10586

Middle Eastern (MID) AF: 0.133 AC: 39 AN: 294

European-Non Finnish (NFE) AF: 0.0742 AC: 5043 AN: 67998

Other (OTH) AF: 0.139 AC: 293 AN: 2112

Alfa AF: 0.102 Hom.: 159

Bravo AF: 0.159

Asia WGS AF: 0.0760 AC: 264 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	2.1
DANN	Benign	0.46
PhyloP100		-0.15

Splicing

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

Other links and lift over

dbSNP: rs8050896; hg19: chr16-66158736;