rs2967340

Variant names:

• chr16-82223946-G-A
• rs2967340
• ENST00000830022.1:n.494-17546G>A

Your query was ambiguous. Multiple possible variants found:

• chr16-82223946-G-A
• chr16-82223946-G-C

Variant summary

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

The ENST00000830022.1(MPHOSPH6-DT):​n.494-17546G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.626 in 152,062 control chromosomes in the GnomAD database, including 35,618 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 0.63 (35618 hom., cov: 32)
• Consequence: MPHOSPH6-DT ENST00000830022.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.948
• Publications: 5 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=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.852 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.494-17546G>A		intron_variant	Intron 4 of 6

Frequencies

GnomAD3 genomes AF: 0.626 AC: 95189 AN: 151944 Hom.: 35613 Cov.: 32

Gnomad AFR AF: 0.212

Gnomad AMI AF: 0.779

Gnomad AMR AF: 0.569

Gnomad ASJ AF: 0.772

Gnomad EAS AF: 0.650

Gnomad SAS AF: 0.564

Gnomad FIN AF: 0.788

Gnomad MID AF: 0.624

Gnomad NFE AF: 0.858

Gnomad OTH AF: 0.674

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

GnomAD4 genome AF: 0.626 AC: 95191 AN: 152062 Hom.: 35618 Cov.: 32 AF XY: 0.620 AC XY: 46086 AN XY: 74320

African (AFR) AF: 0.212 AC: 8767 AN: 41444

American (AMR) AF: 0.568 AC: 8679 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.772 AC: 2682 AN: 3472

East Asian (EAS) AF: 0.650 AC: 3357 AN: 5162

South Asian (SAS) AF: 0.566 AC: 2726 AN: 4818

European-Finnish (FIN) AF: 0.788 AC: 8325 AN: 10564

Middle Eastern (MID) AF: 0.623 AC: 182 AN: 292

European-Non Finnish (NFE) AF: 0.858 AC: 58339 AN: 68012

Other (OTH) AF: 0.676 AC: 1425 AN: 2108

Alfa AF: 0.770 Hom.: 119258

Bravo AF: 0.594

Asia WGS AF: 0.564 AC: 1961 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.1
DANN	Benign	0.44
PhyloP100		-0.95

Splicing

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

Other links and lift over

dbSNP: rs2967340; hg19: chr16-82257551;