16-82176256-A-G

Variant names:

• chr16-82176256-A-G
• rs2967374
• ENST00000830022.1:n.64-2374A>G

Variant summary

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

The ENST00000830022.1(MPHOSPH6-DT):​n.64-2374A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.844 in 152,218 control chromosomes in the GnomAD database, including 54,610 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 0.84 (54610 hom., cov: 32)
• Consequence: MPHOSPH6-DT ENST00000830022.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0280
• Publications: 13 publications found

Genes affected

MPHOSPH6-DT (HGNC:55377): (MPHOSPH6 divergent transcript)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.941 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000830022.1. 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
	MPHOSPH6-DT	ENST00000830022.1		n.64-2374A>G		intron	N/A
	MPHOSPH6-DT	ENST00000830023.1		n.62-2374A>G		intron	N/A
	MPHOSPH6-DT	ENST00000830024.1		n.25-2374A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.844 AC: 128367 AN: 152100 Hom.: 54553 Cov.: 32

Gnomad AFR AF: 0.949

Gnomad AMI AF: 0.954

Gnomad AMR AF: 0.860

Gnomad ASJ AF: 0.784

Gnomad EAS AF: 0.855

Gnomad SAS AF: 0.838

Gnomad FIN AF: 0.844

Gnomad MID AF: 0.816

Gnomad NFE AF: 0.778

Gnomad OTH AF: 0.826

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

GnomAD4 genome AF: 0.844 AC: 128482 AN: 152218 Hom.: 54610 Cov.: 32 AF XY: 0.849 AC XY: 63143 AN XY: 74412

African (AFR) AF: 0.949 AC: 39423 AN: 41548

American (AMR) AF: 0.861 AC: 13151 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.784 AC: 2721 AN: 3472

East Asian (EAS) AF: 0.855 AC: 4432 AN: 5184

South Asian (SAS) AF: 0.838 AC: 4043 AN: 4824

European-Finnish (FIN) AF: 0.844 AC: 8943 AN: 10594

Middle Eastern (MID) AF: 0.816 AC: 240 AN: 294

European-Non Finnish (NFE) AF: 0.778 AC: 52921 AN: 67994

Other (OTH) AF: 0.822 AC: 1738 AN: 2114

Alfa AF: 0.768 Hom.: 2674

Bravo AF: 0.847

Asia WGS AF: 0.847 AC: 2942 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	5.9
DANN	Benign	0.70
PhyloP100		0.028

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: rs2967374;

hg19: chr16-82209861;