16-82191961-A-T

Variant names:

• chr16-82191961-A-T
• rs1862819
• ENST00000830022.1:n.412-3567A>T

Variant summary

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

The ENST00000830022.1(MPHOSPH6-DT):​n.412-3567A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.483 in 152,016 control chromosomes in the GnomAD database, including 22,795 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 0.48 (22795 hom., cov: 32)
• Consequence: MPHOSPH6-DT ENST00000830022.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.221
• Publications: 6 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=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.85 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.412-3567A>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.482 AC: 73276 AN: 151900 Hom.: 22730 Cov.: 32

Gnomad AFR AF: 0.857

Gnomad AMI AF: 0.297

Gnomad AMR AF: 0.522

Gnomad ASJ AF: 0.358

Gnomad EAS AF: 0.651

Gnomad SAS AF: 0.593

Gnomad FIN AF: 0.333

Gnomad MID AF: 0.509

Gnomad NFE AF: 0.259

Gnomad OTH AF: 0.428

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

GnomAD4 genome AF: 0.483 AC: 73400 AN: 152016 Hom.: 22795 Cov.: 32 AF XY: 0.492 AC XY: 36535 AN XY: 74284

African (AFR) AF: 0.857 AC: 35553 AN: 41484

American (AMR) AF: 0.523 AC: 7976 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.358 AC: 1243 AN: 3468

East Asian (EAS) AF: 0.651 AC: 3361 AN: 5164

South Asian (SAS) AF: 0.593 AC: 2857 AN: 4820

European-Finnish (FIN) AF: 0.333 AC: 3510 AN: 10548

Middle Eastern (MID) AF: 0.514 AC: 151 AN: 294

European-Non Finnish (NFE) AF: 0.259 AC: 17581 AN: 67960

Other (OTH) AF: 0.426 AC: 898 AN: 2108

Alfa AF: 0.191 Hom.: 375

Bravo AF: 0.512

Asia WGS AF: 0.589 AC: 2048 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	2.4
DANN	Benign	0.69
PhyloP100		-0.22

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: rs1862819;

hg19: chr16-82225566;