rs1862820

chr16-82174677-G-Cchr16-82174677-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000563841.1(MPHOSPH6-DT):n.53-755G>C variant causes a intron, non coding transcript 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, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.518

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MPHOSPH6-DT	ENST00000563841.1	n.53-755G>C		intron_variant, non_coding_transcript_variant		3

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

Gnomad4 AFR AF: 0.587

Gnomad4 AMR AF: 0.478

Gnomad4 ASJ AF: 0.622

Gnomad4 EAS AF: 0.439

Gnomad4 SAS AF: 0.523

Gnomad4 FIN AF: 0.698

Gnomad4 NFE AF: 0.644

Gnomad4 OTH AF: 0.590

Alfa AF: 0.617 Hom.: 3622

Bravo AF: 0.587

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
Cadd	Benign	2.3
Dann	Benign	0.36

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1862820; hg19: chr16-82208282;