rs16880441

Variant names:

• chr6-88266258-C-G
• rs16880441
• ENST00000648572.1:n.990+14556G>C

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000648572.1(ENSG00000234426):​n.990+14556G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0823 in 151,814 control chromosomes in the GnomAD database, including 552 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 0.082 (552 hom., cov: 32)
• Consequence: ENSG00000234426 ENST00000648572.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.10
• Publications: 7 publications found

Genes affected

ENSG00000234426 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.2).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.1 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000648572.1. 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
	ENSG00000234426	ENST00000648572.1		n.990+14556G>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0823 AC: 12481 AN: 151698 Hom.: 548 Cov.: 32

Gnomad AFR AF: 0.0764

Gnomad AMI AF: 0.0779

Gnomad AMR AF: 0.102

Gnomad ASJ AF: 0.0519

Gnomad EAS AF: 0.107

Gnomad SAS AF: 0.0727

Gnomad FIN AF: 0.120

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.0760

Gnomad OTH AF: 0.0817

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

GnomAD4 genome AF: 0.0823 AC: 12494 AN: 151814 Hom.: 552 Cov.: 32 AF XY: 0.0846 AC XY: 6275 AN XY: 74172

African (AFR) AF: 0.0762 AC: 3154 AN: 41376

American (AMR) AF: 0.102 AC: 1556 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.0519 AC: 180 AN: 3470

East Asian (EAS) AF: 0.107 AC: 553 AN: 5150

South Asian (SAS) AF: 0.0721 AC: 347 AN: 4810

European-Finnish (FIN) AF: 0.120 AC: 1257 AN: 10474

Middle Eastern (MID) AF: 0.0714 AC: 21 AN: 294

European-Non Finnish (NFE) AF: 0.0760 AC: 5167 AN: 67962

Other (OTH) AF: 0.0889 AC: 188 AN: 2114

Alfa AF: 0.0828 Hom.: 363

Bravo AF: 0.0825

Asia WGS AF: 0.133 AC: 462 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.20
CADD	Benign	20
DANN	Benign	0.77
PhyloP100		2.1

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: rs16880441;

hg19: chr6-88975977;