16-82174677-G-C

Variant names:

• chr16-82174677-G-C
• rs1862820
• ENST00000563841.1:n.53-755G>C

Variant summary

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

The ENST00000563841.1(MPHOSPH6-DT):​n.53-755G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.604 in 151,976 control chromosomes in the GnomAD database, including 28,169 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 0.60 (28169 hom., cov: 32)
• Consequence: MPHOSPH6-DT ENST00000563841.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.518
• Publications: 8 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=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.639 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000563841.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MPHOSPH6-DT	ENST00000563841.1	TSL:3	n.53-755G>C		intron	N/A
	MPHOSPH6-DT	ENST00000830022.1		n.64-3953G>C		intron	N/A
	MPHOSPH6-DT	ENST00000830023.1		n.62-3953G>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.604 AC: 91763 AN: 151856 Hom.: 28147 Cov.: 32

Gnomad AFR AF: 0.587

Gnomad AMI AF: 0.826

Gnomad AMR AF: 0.479

Gnomad ASJ AF: 0.622

Gnomad EAS AF: 0.439

Gnomad SAS AF: 0.523

Gnomad FIN AF: 0.698

Gnomad MID AF: 0.545

Gnomad NFE AF: 0.644

Gnomad OTH AF: 0.594

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

GnomAD4 genome AF: 0.604 AC: 91822 AN: 151976 Hom.: 28169 Cov.: 32 AF XY: 0.603 AC XY: 44798 AN XY: 74266

African (AFR) AF: 0.587 AC: 24310 AN: 41428

American (AMR) AF: 0.478 AC: 7294 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.622 AC: 2160 AN: 3472

East Asian (EAS) AF: 0.439 AC: 2272 AN: 5172

South Asian (SAS) AF: 0.523 AC: 2523 AN: 4828

European-Finnish (FIN) AF: 0.698 AC: 7357 AN: 10542

Middle Eastern (MID) AF: 0.544 AC: 160 AN: 294

European-Non Finnish (NFE) AF: 0.644 AC: 43749 AN: 67952

Other (OTH) AF: 0.590 AC: 1244 AN: 2110

Alfa AF: 0.617 Hom.: 3622

Bravo AF: 0.587

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	2.3
DANN	Benign	0.36
PhyloP100		0.52

Splicing

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

Other links and lift over

dbSNP: rs1862820; hg19: chr16-82208282;