chr17-44668776-C-T

Variant names:

• chr17-44668776-C-T
• rs8079488
• NM_001145080.3:c.2322+543C>T

Variant summary

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

The NM_001145080.3(MEIOC):​c.2322+543C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0871 in 152,200 control chromosomes in the GnomAD database, including 629 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 0.087 (629 hom., cov: 32)
• Consequence: MEIOC NM_001145080.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.34
• Publications: 1 publications found

Genes affected

MEIOC (HGNC:26670): (meiosis specific with coiled-coil domain) Predicted to be involved in several processes, including gamete generation; germline cell cycle switching, mitotic to meiotic cell cycle; and mRNA stabilization. Predicted to be active in cytoplasm and nucleus. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.135 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MEIOC	NM_001145080.3	c.2322+543C>T		intron_variant	Intron 5 of 7	ENST00000409122.7	NP_001138552.2
MEIOC	XM_005257236.4	c.2322+543C>T		intron_variant	Intron 5 of 8		XP_005257293.1
MEIOC	XM_047435802.1	c.2321+544C>T		intron_variant	Intron 5 of 5		XP_047291758.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MEIOC	ENST00000409122.7	c.2322+543C>T		intron_variant	Intron 5 of 7	5	NM_001145080.3	ENSP00000386452.1
MEIOC	ENST00000409464.1	c.1824+543C>T		intron_variant	Intron 2 of 2	2		ENSP00000386586.1
MEIOC	ENST00000472403.5	n.12+543C>T		intron_variant	Intron 1 of 10	2		ENSP00000467305.1

Frequencies

GnomAD3 genomes AF: 0.0871 AC: 13252 AN: 152082 Hom.: 627 Cov.: 32

Gnomad AFR AF: 0.0660

Gnomad AMI AF: 0.0143

Gnomad AMR AF: 0.0732

Gnomad ASJ AF: 0.0683

Gnomad EAS AF: 0.144

Gnomad SAS AF: 0.0881

Gnomad FIN AF: 0.117

Gnomad MID AF: 0.0949

Gnomad NFE AF: 0.0960

Gnomad OTH AF: 0.0879

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

GnomAD4 genome AF: 0.0871 AC: 13260 AN: 152200 Hom.: 629 Cov.: 32 AF XY: 0.0878 AC XY: 6532 AN XY: 74388

African (AFR) AF: 0.0660 AC: 2742 AN: 41530

American (AMR) AF: 0.0731 AC: 1118 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.0683 AC: 237 AN: 3472

East Asian (EAS) AF: 0.144 AC: 747 AN: 5188

South Asian (SAS) AF: 0.0884 AC: 426 AN: 4820

European-Finnish (FIN) AF: 0.117 AC: 1232 AN: 10568

Middle Eastern (MID) AF: 0.0952 AC: 28 AN: 294

European-Non Finnish (NFE) AF: 0.0960 AC: 6530 AN: 67998

Other (OTH) AF: 0.0884 AC: 187 AN: 2116

Alfa AF: 0.0946 Hom.: 1408

Bravo AF: 0.0817

Asia WGS AF: 0.0960 AC: 334 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.9
DANN	Benign	0.42
PhyloP100		-1.3
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs8079488; hg19: chr17-42746144;