chr7-36221115-A-G

Variant names:

• chr7-36221115-A-G
• rs2540678
• NM_030636.3:c.879-17870A>G

Variant summary

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

The NM_030636.3(EEPD1):​c.879-17870A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.709 in 152,196 control chromosomes in the GnomAD database, including 39,309 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 0.71 (39309 hom., cov: 34)
• Consequence: EEPD1 NM_030636.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.494
• Publications: 2 publications found

Genes affected

EEPD1 (HGNC:22223): (endonuclease/exonuclease/phosphatase family domain containing 1) Predicted to enable DNA binding activity. Involved in positive regulation of cholesterol efflux. Is anchored component of plasma membrane. [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=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.782 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
EEPD1	NM_030636.3	c.879-17870A>G		intron_variant	Intron 2 of 7	ENST00000242108.9	NP_085139.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
EEPD1	ENST00000242108.9	c.879-17870A>G		intron_variant	Intron 2 of 7	1	NM_030636.3	ENSP00000242108.4

Frequencies

GnomAD3 genomes AF: 0.709 AC: 107843 AN: 152078 Hom.: 39297 Cov.: 34

Gnomad AFR AF: 0.548

Gnomad AMI AF: 0.813

Gnomad AMR AF: 0.786

Gnomad ASJ AF: 0.809

Gnomad EAS AF: 0.473

Gnomad SAS AF: 0.620

Gnomad FIN AF: 0.835

Gnomad MID AF: 0.722

Gnomad NFE AF: 0.788

Gnomad OTH AF: 0.716

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

GnomAD4 genome AF: 0.709 AC: 107892 AN: 152196 Hom.: 39309 Cov.: 34 AF XY: 0.710 AC XY: 52855 AN XY: 74412

African (AFR) AF: 0.548 AC: 22736 AN: 41488

American (AMR) AF: 0.786 AC: 12021 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.809 AC: 2808 AN: 3470

East Asian (EAS) AF: 0.473 AC: 2450 AN: 5184

South Asian (SAS) AF: 0.621 AC: 2998 AN: 4828

European-Finnish (FIN) AF: 0.835 AC: 8850 AN: 10604

Middle Eastern (MID) AF: 0.718 AC: 211 AN: 294

European-Non Finnish (NFE) AF: 0.788 AC: 53574 AN: 68010

Other (OTH) AF: 0.712 AC: 1503 AN: 2112

Alfa AF: 0.764 Hom.: 28945

Bravo AF: 0.698

Asia WGS AF: 0.514 AC: 1790 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.63
DANN	Benign	0.50
PhyloP100		-0.49
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs2540678; hg19: chr7-36260724;