7-36172140-C-T

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
EEPD1	NM_030636.3	c.878+16938C>T		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.878+16938C>T		intron_variant	Intron 2 of 7	1	NM_030636.3	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

Gnomad4 AFR AF: 0.220

Gnomad4 AMR AF: 0.127

Gnomad4 ASJ AF: 0.108

Gnomad4 EAS AF: 0.142

Gnomad4 SAS AF: 0.110

Gnomad4 FIN AF: 0.230

Gnomad4 NFE AF: 0.156

Gnomad4 OTH AF: 0.161

Alfa AF: 0.146 Hom.: 1799

Bravo AF: 0.167

Asia WGS AF: 0.139 AC: 488 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.66
DANN	Benign	0.39

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

Publications

LitVar

Other links and lift over

dbSNP: rs9648428; hg19: chr7-36211749;