16-82560778-T-C

Variant names:

• chr16-82560778-T-C
• rs4783227
• ENST00000565374.2:n.613-6530A>G

Variant summary

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

The ENST00000565374.2(ENSG00000261285):​n.613-6530A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.433 in 152,104 control chromosomes in the GnomAD database, including 16,905 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 0.43 (16905 hom., cov: 33)
• Consequence: ENSG00000261285 ENST00000565374.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.280
• Publications: 13 publications found

Genes affected

ENSG00000261285 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.581 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000565374.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LOC101928392	NR_188568.1		n.544-6530A>G		intron	N/A
	LOC101928392	NR_188569.1		n.543+14012A>G		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000261285	ENST00000565374.2	TSL:3	n.613-6530A>G		intron	N/A
	ENSG00000261285	ENST00000650164.1		n.584+14012A>G		intron	N/A
	ENSG00000307474	ENST00000826480.1		n.38+9636T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.433 AC: 65873 AN: 151986 Hom.: 16912 Cov.: 33

Gnomad AFR AF: 0.149

Gnomad AMI AF: 0.510

Gnomad AMR AF: 0.376

Gnomad ASJ AF: 0.475

Gnomad EAS AF: 0.422

Gnomad SAS AF: 0.455

Gnomad FIN AF: 0.618

Gnomad MID AF: 0.509

Gnomad NFE AF: 0.586

Gnomad OTH AF: 0.450

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

GnomAD4 genome AF: 0.433 AC: 65850 AN: 152104 Hom.: 16905 Cov.: 33 AF XY: 0.432 AC XY: 32131 AN XY: 74346

African (AFR) AF: 0.149 AC: 6189 AN: 41536

American (AMR) AF: 0.375 AC: 5737 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.475 AC: 1649 AN: 3468

East Asian (EAS) AF: 0.422 AC: 2181 AN: 5168

South Asian (SAS) AF: 0.456 AC: 2198 AN: 4820

European-Finnish (FIN) AF: 0.618 AC: 6527 AN: 10558

Middle Eastern (MID) AF: 0.503 AC: 148 AN: 294

European-Non Finnish (NFE) AF: 0.586 AC: 39815 AN: 67950

Other (OTH) AF: 0.445 AC: 942 AN: 2116

Alfa AF: 0.530 Hom.: 99915

Bravo AF: 0.405

Asia WGS AF: 0.381 AC: 1325 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	4.8
DANN	Benign	0.67
PhyloP100		-0.28

Splicing

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

Other links and lift over

dbSNP: rs4783227; hg19: chr16-82594383;