1-53076861-G-T

Variant names:

• chr1-53076861-G-T
• rs1077467
• NM_153703.5:c.582-329G>T

Variant summary

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

The NM_153703.5(PODN):​c.582-329G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0626 in 152,202 control chromosomes in the GnomAD database, including 579 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 0.063 (579 hom., cov: 32)
• Consequence: PODN NM_153703.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.215
• Publications: 2 publications found

Genes affected

PODN (HGNC:23174): (podocan) The protein encoded by this gene is a member of the small leucine-rich repeat protein family and contains an amino terminal CX3CXCX7C cysteine-rich cluster followed by a leucine-rich repeat domain. Studies suggest that this protein could function to inhibit smooth muscle cell proliferation and migration following arterial injury. [provided by RefSeq, Jul 2016]

ENSG00000232993 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.232 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PODN	NM_153703.5	c.582-329G>T		intron_variant	Intron 5 of 10	ENST00000312553.10	NP_714914.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PODN	ENST00000312553.10	c.582-329G>T		intron_variant	Intron 5 of 10	1	NM_153703.5	ENSP00000308315.6

Frequencies

GnomAD3 genomes AF: 0.0625 AC: 9511 AN: 152084 Hom.: 575 Cov.: 32

Gnomad AFR AF: 0.113

Gnomad AMI AF: 0.0384

Gnomad AMR AF: 0.0919

Gnomad ASJ AF: 0.0150

Gnomad EAS AF: 0.243

Gnomad SAS AF: 0.147

Gnomad FIN AF: 0.0247

Gnomad MID AF: 0.0285

Gnomad NFE AF: 0.0148

Gnomad OTH AF: 0.0535

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

GnomAD4 genome AF: 0.0626 AC: 9531 AN: 152202 Hom.: 579 Cov.: 32 AF XY: 0.0650 AC XY: 4836 AN XY: 74414

African (AFR) AF: 0.113 AC: 4685 AN: 41500

American (AMR) AF: 0.0920 AC: 1408 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.0150 AC: 52 AN: 3468

East Asian (EAS) AF: 0.243 AC: 1254 AN: 5152

South Asian (SAS) AF: 0.146 AC: 704 AN: 4820

European-Finnish (FIN) AF: 0.0247 AC: 262 AN: 10626

Middle Eastern (MID) AF: 0.0272 AC: 8 AN: 294

European-Non Finnish (NFE) AF: 0.0148 AC: 1006 AN: 68014

Other (OTH) AF: 0.0553 AC: 117 AN: 2116

Alfa AF: 0.0364 Hom.: 471

Bravo AF: 0.0696

Asia WGS AF: 0.207 AC: 718 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	5.2
DANN	Benign	0.72
PhyloP100		-0.21
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: rs1077467; hg19: chr1-53542533; COSMIC: COSV107356426; COSMIC: COSV107356426;