rs1862820

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

• chr16-82174677-G-C
• chr16-82174677-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 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

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MPHOSPH6-DT	ENST00000563841.1	n.53-755G>C		intron_variant	Intron 1 of 1	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;