chr7-36172140-C-T

Variant names:

• chr7-36172140-C-T
• rs9648428
• NM_030636.3:c.878+16938C>T

Variant summary

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

The NM_030636.3(EEPD1):​c.878+16938C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.173 in 152,062 control chromosomes in the GnomAD database, including 2,410 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 0.17 (2410 hom., cov: 32)
• Consequence: EEPD1 NM_030636.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.71
• Publications: 6 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=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.216 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_030636.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	EEPD1	NM_030636.3	MANE Select	c.878+16938C>T		intron	N/A	NP_085139.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	EEPD1	ENST00000242108.9	TSL:1 MANE Select	c.878+16938C>T		intron	N/A	ENSP00000242108.4

Frequencies

GnomAD3 genomes AF: 0.173 AC: 26271 AN: 151944 Hom.: 2406 Cov.: 32

Gnomad AFR AF: 0.220

Gnomad AMI AF: 0.173

Gnomad AMR AF: 0.127

Gnomad ASJ AF: 0.108

Gnomad EAS AF: 0.142

Gnomad SAS AF: 0.111

Gnomad FIN AF: 0.230

Gnomad MID AF: 0.161

Gnomad NFE AF: 0.156

Gnomad OTH AF: 0.160

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

GnomAD4 genome AF: 0.173 AC: 26301 AN: 152062 Hom.: 2410 Cov.: 32 AF XY: 0.175 AC XY: 12970 AN XY: 74326

African (AFR) AF: 0.220 AC: 9120 AN: 41458

American (AMR) AF: 0.127 AC: 1937 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.108 AC: 374 AN: 3470

East Asian (EAS) AF: 0.142 AC: 734 AN: 5180

South Asian (SAS) AF: 0.110 AC: 532 AN: 4824

European-Finnish (FIN) AF: 0.230 AC: 2432 AN: 10570

Middle Eastern (MID) AF: 0.167 AC: 49 AN: 294

European-Non Finnish (NFE) AF: 0.156 AC: 10625 AN: 67962

Other (OTH) AF: 0.161 AC: 340 AN: 2112

Alfa AF: 0.156 Hom.: 5467

Bravo AF: 0.167

Asia WGS AF: 0.139 AC: 488 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.66
DANN	Benign	0.39
PhyloP100		-1.7
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: rs9648428; hg19: chr7-36211749;