rs2354025

Variant names:

• chr16-86633803-C-T
• rs2354025
• ENST00000808928.1:n.121-11413C>T

Variant summary

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

The ENST00000808928.1(ENSG00000261161):​n.121-11413C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.284 in 152,124 control chromosomes in the GnomAD database, including 6,900 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 0.28 (6900 hom., cov: 32)
• Consequence: ENSG00000261161 ENST00000808928.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.303
• Publications: 0 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=-0.77).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.615 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000808928.1. 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	ENST00000808928.1		n.121-11413C>T		intron	N/A
	ENSG00000261161	ENST00000808929.1		n.145-11413C>T		intron	N/A
	ENSG00000261161	ENST00000808930.1		n.113+2997C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.284 AC: 43211 AN: 152006 Hom.: 6895 Cov.: 32

Gnomad AFR AF: 0.159

Gnomad AMI AF: 0.366

Gnomad AMR AF: 0.277

Gnomad ASJ AF: 0.268

Gnomad EAS AF: 0.632

Gnomad SAS AF: 0.303

Gnomad FIN AF: 0.355

Gnomad MID AF: 0.287

Gnomad NFE AF: 0.323

Gnomad OTH AF: 0.279

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

GnomAD4 genome AF: 0.284 AC: 43239 AN: 152124 Hom.: 6900 Cov.: 32 AF XY: 0.287 AC XY: 21314 AN XY: 74364

African (AFR) AF: 0.159 AC: 6610 AN: 41502

American (AMR) AF: 0.277 AC: 4236 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.268 AC: 930 AN: 3468

East Asian (EAS) AF: 0.633 AC: 3263 AN: 5158

South Asian (SAS) AF: 0.304 AC: 1465 AN: 4820

European-Finnish (FIN) AF: 0.355 AC: 3760 AN: 10582

Middle Eastern (MID) AF: 0.284 AC: 83 AN: 292

European-Non Finnish (NFE) AF: 0.323 AC: 21963 AN: 67992

Other (OTH) AF: 0.282 AC: 596 AN: 2114

Alfa AF: 0.305 Hom.: 11865

Bravo AF: 0.274

Asia WGS AF: 0.408 AC: 1418 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	1.1
DANN	Benign	0.76
PhyloP100		-0.30

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs2354025;

hg19: chr16-86667409;