16-82196787-T-G

Variant names:

• chr16-82196787-T-G
• rs2967391
• ENST00000830022.1:n.493+1178T>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.493+1178T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.362 in 151,978 control chromosomes in the GnomAD database, including 14,662 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 0.36 (14662 hom., cov: 32)
• Consequence: MPHOSPH6-DT ENST00000830022.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0920
• Publications: 9 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 = 0.721 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MPHOSPH6-DT	ENST00000830022.1	n.493+1178T>G		intron_variant	Intron 4 of 6

Frequencies

GnomAD3 genomes AF: 0.362 AC: 54910 AN: 151860 Hom.: 14613 Cov.: 32

Gnomad AFR AF: 0.727

Gnomad AMI AF: 0.219

Gnomad AMR AF: 0.438

Gnomad ASJ AF: 0.228

Gnomad EAS AF: 0.410

Gnomad SAS AF: 0.447

Gnomad FIN AF: 0.213

Gnomad MID AF: 0.367

Gnomad NFE AF: 0.146

Gnomad OTH AF: 0.313

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

GnomAD4 genome AF: 0.362 AC: 55014 AN: 151978 Hom.: 14662 Cov.: 32 AF XY: 0.368 AC XY: 27350 AN XY: 74272

African (AFR) AF: 0.727 AC: 30148 AN: 41446

American (AMR) AF: 0.439 AC: 6703 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.228 AC: 792 AN: 3468

East Asian (EAS) AF: 0.409 AC: 2112 AN: 5162

South Asian (SAS) AF: 0.445 AC: 2142 AN: 4810

European-Finnish (FIN) AF: 0.213 AC: 2250 AN: 10562

Middle Eastern (MID) AF: 0.367 AC: 108 AN: 294

European-Non Finnish (NFE) AF: 0.146 AC: 9903 AN: 67952

Other (OTH) AF: 0.311 AC: 657 AN: 2112

Alfa AF: 0.246 Hom.: 15721

Bravo AF: 0.392

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.8
DANN	Benign	0.34
PhyloP100		0.092

Splicing

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

Other links and lift over

dbSNP: rs2967391; hg19: chr16-82230392;