chr10-44976597-A-G

Position:

• chr10-44976597-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_007021.4(DEPP1):​c.*795T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.728 in 152,644 control chromosomes in the GnomAD database, including 40,584 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 0.73 (40461 hom., cov: 33)
  • Exomes 𝑓: 0.72 (123 hom.)
• Consequence: DEPP1 NM_007021.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.06

Genes affected

DEPP1 (HGNC:23355): (DEPP autophagy regulator 1) The expression of this gene is induced by fasting as well as by progesterone. The protein encoded by this gene contains a t-synaptosome-associated protein receptor (SNARE) coiled-coil homology domain and a peroxisomal targeting signal. Production of the encoded protein leads to phosphorylation and activation of the transcription factor ELK1. [provided by RefSeq, Jul 2008]

RASSF4 (HGNC:20793): (Ras association domain family member 4) The function of this gene has not yet been determined but may involve a role in tumor suppression. Alternative splicing of this gene results in several transcript variants; however, most of the variants have not been fully described. [provided by RefSeq, Jul 2008]

RASSF4 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.772 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
DEPP1	NM_007021.4	c.*795T>C		3_prime_UTR_variant	2/2	ENST00000298295.4	NP_008952.1
RASSF4	NM_032023.4	c.138+4749A>G		intron_variant		ENST00000340258.10	NP_114412.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
DEPP1	ENST00000298295	c.*795T>C		3_prime_UTR_variant	2/2	1	NM_007021.4	ENSP00000298295.3
RASSF4	ENST00000340258.10	c.138+4749A>G		intron_variant		1	NM_032023.4	ENSP00000339692.4

Frequencies

GnomAD3 genomes AF: 0.728 AC: 110738 AN: 152072 Hom.: 40418 Cov.: 33

Gnomad AFR AF: 0.720

Gnomad AMI AF: 0.556

Gnomad AMR AF: 0.784

Gnomad ASJ AF: 0.634

Gnomad EAS AF: 0.776

Gnomad SAS AF: 0.764

Gnomad FIN AF: 0.749

Gnomad MID AF: 0.617

Gnomad NFE AF: 0.719

Gnomad OTH AF: 0.725

GnomAD4 exome AF: 0.722 AC: 328 AN: 454 Hom.: 123 Cov.: 0 AF XY: 0.738 AC XY: 242 AN XY: 328

Gnomad4 AFR exome AF: 0.750

Gnomad4 AMR exome AF: 0.667

Gnomad4 ASJ exome AF: 0.500

Gnomad4 EAS exome AF: 0.800

Gnomad4 SAS exome AF: 1.00

Gnomad4 FIN exome AF: 0.625

Gnomad4 NFE exome AF: 0.729

Gnomad4 OTH exome AF: 0.700

GnomAD4 genome AF: 0.728 AC: 110843 AN: 152190 Hom.: 40461 Cov.: 33 AF XY: 0.733 AC XY: 54514 AN XY: 74398

Gnomad4 AFR AF: 0.720

Gnomad4 AMR AF: 0.784

Gnomad4 ASJ AF: 0.634

Gnomad4 EAS AF: 0.776

Gnomad4 SAS AF: 0.762

Gnomad4 FIN AF: 0.749

Gnomad4 NFE AF: 0.719

Gnomad4 OTH AF: 0.728

Alfa AF: 0.720 Hom.: 8791

Bravo AF: 0.732

Asia WGS AF: 0.783 AC: 2725 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	0.69
DANN	Benign	0.51

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: rs7013; hg19: chr10-45472045; COSMIC: COSV53575211; COSMIC: COSV53575211;