16-82576112-T-C

Variant names:

• chr16-82576112-T-C
• rs4782717
• ENST00000826480.1:n.38+24970T>C

Variant summary

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

The ENST00000826480.1(ENSG00000307474):​n.38+24970T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.736 in 152,176 control chromosomes in the GnomAD database, including 41,338 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 (41338 hom., cov: 33)
• Consequence: ENSG00000307474 ENST00000826480.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0640
• Publications: 5 publications found

Genes affected

ENSG00000307474 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.834 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
ENSG00000307474	ENST00000826480.1	n.38+24970T>C		intron_variant	Intron 1 of 2
ENSG00000307496	ENST00000826593.1	n.133+388T>C		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.736 AC: 111878 AN: 152058 Hom.: 41292 Cov.: 33

Gnomad AFR AF: 0.721

Gnomad AMI AF: 0.573

Gnomad AMR AF: 0.845

Gnomad ASJ AF: 0.782

Gnomad EAS AF: 0.753

Gnomad SAS AF: 0.749

Gnomad FIN AF: 0.679

Gnomad MID AF: 0.918

Gnomad NFE AF: 0.724

Gnomad OTH AF: 0.781

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

GnomAD4 genome AF: 0.736 AC: 111981 AN: 152176 Hom.: 41338 Cov.: 33 AF XY: 0.737 AC XY: 54828 AN XY: 74392

African (AFR) AF: 0.721 AC: 29905 AN: 41490

American (AMR) AF: 0.846 AC: 12942 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.782 AC: 2716 AN: 3472

East Asian (EAS) AF: 0.753 AC: 3902 AN: 5182

South Asian (SAS) AF: 0.750 AC: 3623 AN: 4828

European-Finnish (FIN) AF: 0.679 AC: 7192 AN: 10586

Middle Eastern (MID) AF: 0.915 AC: 269 AN: 294

European-Non Finnish (NFE) AF: 0.724 AC: 49252 AN: 67996

Other (OTH) AF: 0.784 AC: 1657 AN: 2114

Alfa AF: 0.741 Hom.: 69890

Bravo AF: 0.749

Asia WGS AF: 0.766 AC: 2664 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	6.1
DANN	Benign	0.48
PhyloP100		0.064

Splicing

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

Other links and lift over

dbSNP: rs4782717; hg19: chr16-82609717;