16-86661574-A-T

Variant names:

• chr16-86661574-A-T
• rs299941
• ENST00000565822.1:n.328-7169A>T

Variant summary

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

The ENST00000565822.1(ENSG00000261161):​n.328-7169A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.117 in 152,102 control chromosomes in the GnomAD database, including 1,860 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 0.12 (1860 hom., cov: 32)
• Consequence: ENSG00000261161 ENST00000565822.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.21
• Publications: 2 publications found

Genes affected

ENSG00000261161 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.256 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000565822.1. 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
	ENSG00000261161	ENST00000565822.1	TSL:3	n.328-7169A>T		intron	N/A
	ENSG00000261161	ENST00000808928.1		n.854+14218A>T		intron	N/A
	ENSG00000261161	ENST00000808929.1		n.721+14375A>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.117 AC: 17838 AN: 151986 Hom.: 1854 Cov.: 32

Gnomad AFR AF: 0.224

Gnomad AMI AF: 0.0537

Gnomad AMR AF: 0.262

Gnomad ASJ AF: 0.0922

Gnomad EAS AF: 0.0994

Gnomad SAS AF: 0.0825

Gnomad FIN AF: 0.0390

Gnomad MID AF: 0.0791

Gnomad NFE AF: 0.0381

Gnomad OTH AF: 0.121

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

GnomAD4 genome AF: 0.117 AC: 17865 AN: 152102 Hom.: 1860 Cov.: 32 AF XY: 0.120 AC XY: 8895 AN XY: 74326

African (AFR) AF: 0.224 AC: 9297 AN: 41470

American (AMR) AF: 0.263 AC: 4014 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.0922 AC: 320 AN: 3472

East Asian (EAS) AF: 0.0992 AC: 512 AN: 5160

South Asian (SAS) AF: 0.0826 AC: 398 AN: 4816

European-Finnish (FIN) AF: 0.0390 AC: 413 AN: 10590

Middle Eastern (MID) AF: 0.0680 AC: 20 AN: 294

European-Non Finnish (NFE) AF: 0.0381 AC: 2589 AN: 68000

Other (OTH) AF: 0.120 AC: 253 AN: 2110

Alfa AF: 0.0227 Hom.: 27

Bravo AF: 0.141

Asia WGS AF: 0.111 AC: 386 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	4.7
DANN	Benign	0.43
PhyloP100		1.2

Splicing

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

Other links and lift over

dbSNP: rs299941; hg19: chr16-86695180;