ENST00000561657.1:n.381+4821A>G

Variant names:

• chr16-64338708-T-C
• rs1074651
• ENST00000561657.1:n.381+4821A>G

Variant summary

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

The ENST00000561657.1(ENSG00000261028):​n.381+4821A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.369 in 152,008 control chromosomes in the GnomAD database, including 10,756 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 0.37 (10756 hom., cov: 32)
• Consequence: ENSG00000261028 ENST00000561657.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.38
• Publications: 1 publications found

Genes affected

ENSG00000261028 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.446 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000561657.1. 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
	ENSG00000261028	ENST00000561657.1	TSL:3	n.381+4821A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.369 AC: 56070 AN: 151888 Hom.: 10740 Cov.: 32

Gnomad AFR AF: 0.451

Gnomad AMI AF: 0.438

Gnomad AMR AF: 0.412

Gnomad ASJ AF: 0.373

Gnomad EAS AF: 0.348

Gnomad SAS AF: 0.241

Gnomad FIN AF: 0.353

Gnomad MID AF: 0.354

Gnomad NFE AF: 0.323

Gnomad OTH AF: 0.342

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

GnomAD4 genome AF: 0.369 AC: 56128 AN: 152008 Hom.: 10756 Cov.: 32 AF XY: 0.369 AC XY: 27401 AN XY: 74288

African (AFR) AF: 0.451 AC: 18695 AN: 41440

American (AMR) AF: 0.412 AC: 6298 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.373 AC: 1293 AN: 3462

East Asian (EAS) AF: 0.348 AC: 1788 AN: 5140

South Asian (SAS) AF: 0.241 AC: 1159 AN: 4818

European-Finnish (FIN) AF: 0.353 AC: 3726 AN: 10566

Middle Eastern (MID) AF: 0.371 AC: 109 AN: 294

European-Non Finnish (NFE) AF: 0.323 AC: 21946 AN: 67996

Other (OTH) AF: 0.339 AC: 716 AN: 2110

Alfa AF: 0.334 Hom.: 4422

Bravo AF: 0.380

Asia WGS AF: 0.323 AC: 1126 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.35
DANN	Benign	0.66
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs1074651; hg19: chr16-64372612;